professional science master’s in bioinformatics ... · quantitative sciences background to gain...

UNIVERSITY OF DELAWARE

PROFESSIONAL SCIENCE MASTER’S IN

BIOINFORMATICS

COMPUTATIONAL SCIENCES CONCENTRATION

ACADEMIC PROGRAM APPLICATION

FEBRUARY 18, 2010

2

PART I

UNIVERSITY FACULTY

SENATE FORM

3

PROFESSIONAL SCIENCE MASTER’S IN BIOINFORMATICS:

COMPUTATIONAL SCIENCES CONCENTRATION Academic Program Approval This form is a routing document for the approval of new and revised academic programs. Proposing department should complete this form. For more information, call the Faculty Senate Office at 831-2921.

Submitted by: Cathy H. Wu phone number 831-8869 .

Department: Computer & Information Sciences .email address [email protected] .

Action: ____Request for New Professional Science Master’s in Bioinformatics (BINF-PSM), _

Computational Sciences Concentration (CS1) . (Example: add major/minor/concentration, delete major/minor/concentration, revise

major/minor/concentration, academic unit name change, request for permanent status, policy change, etc.)

Effective term___________10F_____________________________________________________________________ (use format 04F, 05W)

Current degree __________N/A____________________________________________________________________ (Example: BA, BACH, BACJ, HBA, EDD, MA, MBA, etc.)

Proposed change leads to the degree of: PSM (Example: BA, BACH, BACJ, HBA, EDD, MA, MBA, etc.)

Proposed name: Professional Science Master’s in Bioinformatics (BINF-PSM), . Computational Sciences Concentration (CS1) . Proposed new name for revised or new major / minor / concentration / academic unit (if applicable)

Revising or Deleting:

Undergraduate major / Concentration:______________________________________ (Example: Applied Music – Instrumental degree BMAS)

Undergraduate minor:____________________________________________________ (Example: African Studies, Business Administration, English, Leadership, etc.)

Graduate Program Policy statement change:_________________________________ (Must attach your Graduate Program Policy Statement)

Graduate Program of Study:______________________________________________ (Example: Animal Science: MS Animal Science: PHD Economics: MA Economics: PHD)

Graduate minor / concentration:___________________________________________

4

Note: all graduate studies proposals must include an electronic copy of the Graduate Program Policy Document, highlighting the changes made to the original policy document. List new courses required for the new or revised curriculum. How do they support the overall program objectives of the major/minor/concentrations)? (Be aware that approval of the curriculum is dependent upon these courses successfully passing through the Course Challenge list. If there are no new courses enter “None”) CISC636: Bioinformatics (3) * submitted for re-title from “Introduction to Bioinformatics” PLSC636: Plant Genes and Genomes (3) * submitted for re-title from “Advanced Plant Genetics” MATH660: Introduction to Systems Biology (3) * adapted from MATH460 STAT613: Multivariate Statistical Methods with Biology Applications (3) * new course being developed BINF864: Internship * new course listing BINF865: Seminar * new course listing BUAD500: Survey of Business (3) * new course being developed STAT670: Introduction to Statistical Analysis I (3) * new course being developed STAT671: Introduction to Statistical Analysis II (3) * new course being developed Explain, when appropriate, how this new/revised curriculum supports the 10 goals of undergraduate education: http://www.ugs.udel.edu/gened/

N/A Identify other units affected by the proposed changes: (Attach permission from the affected units. If no other unit is affected, enter “None”)

College of Arts & Sciences: Department of Biological Sciences Department of Mathematical Sciences

College of Agriculture & Natural Resources Department of Plant & Soil Sciences Department of Food & Resource Economics Department of Animal & Food Sciences

College of Engineering Department of Electrical & Computer Engineering Department of Chemical Engineering

College of Earth, Ocean & Environment Marine Biosciences Program

Alfred Lerner College of Business & Economics Department of Business Administration Department of Accounting & MIS

College of Education & Public Policy School of Urban Affairs & Public Policy

Office of the Vice Provost for Graduate & Professional Education Professional Education Initiatives

Describe the rationale for the proposed program change(s):

5

(Explain your reasons for creating, revising, or deleting the curriculum or program.) The Professional Science Master’s in Bioinformatics (BINF-PSM) will position UD as a regional leader in bioinformatics professional education. The scientific curriculum, together with “Plus” component for professional skills and the immersive Internship will well prepare the BINF-PSM graduates to pursue a career in industry, business, government agencies, or non-profit organizations. The Computational Sciences Concentration (CS1) will allow students with strong quantitative sciences background to gain solid knowledge and industry experience in developing bioinformatics methods, tools and/or databases for modern biotechnology or medicine. Program Requirements: (Show the new or revised curriculum as it should appear in the Course Catalog. If this is a revision, be sure to indicate the changes being made to the current curriculum and include a side-by-side comparison of the credit distribution before and after the proposed change.)

BINF-PSM Computational Sciences Concentration (CS1) – Degree Requirement 42 Credit Hours Total Bioinformatics & Computational Biology Core – Computational Sciences

15 Credits

Ethics Core 3 Credits Electives – Computational Sciences 6 Credits Internship 6 Credits Professional Science Master’s Plus Courses (Business/ industry Track or Government/Non-Profit Track)

12 Credits

BINF-PSM Computational Sciences Concentration (CS1) – Course Curriculum Bioinformatics & Computational Biology Core – Computational Sciences (15) Bioinformatics (3) CISC636: Bioinformatics (3) *

Introduction to Discipline (3) [select one]

ELEG671: Introduction to Biomedical Engineering (3) BISC602: Molecular Biology of Animal Cells (3) BISC612: Advanced Cell Biology (3) BISC654: Biochemical Genetics (3) PLSC636: Plant Genes and Genomes (3) * ANFS670: Principles of Molecular Genetics (3) MAST616: Methods in Molecular Biology (3)

Systems Biology (3) MATH660: Introduction to Systems Biology (3) * Database (3) CISC637: Database Systems (3) Biostatistics (3) [select one]

STAT613: Multivariate Statistical Methods with Biology Applications (3) * STAT656: Biostatistics (3)

Ethics Core (3)

Ethics (3) [select one]

BISC631: Practice of Science (3) UAPP648: Environmental Ethics (3) UAPP650: Values Ethics and Leadership (3) BUAD840: Ethical Issues in Global Business Environments (3)

Electives – Computational Sciences (6) Electives (6) [select two]

CISC841: Algorithms in Bioinformatics (3) CISC621: Algorithm Design and Analysis (3)

6

CISC640: Computer Graphics (3) CISC642: Introduction to Computer Vision (3) CISC650: Computer Networks (3) CISC675: Object Oriented Software Engineering (3) CISC681: Artificial Intelligence (3) CISC683: Introduction to Data mining (3) CISC882: Natural Language Processing (3) CISC886: Multi-Agent Systems (3) CISC887: Internet Information Gathering (3) CISC888: Machine Learning (3) MATH607: Survey of Scientific Computing (3) MATH611: Introduction to Numerical Analysis and Scientific Computing (3)STAT670: Introduction to Statistical Analysis I (3) * STAT671: Introduction to Statistical Analysis II (3) * STAT608: Statistical Research Methods (3) STAT615: Design and Analysis of Experiments (3) STAT619: Time Series Analysis (3) STAT621: Survival analysis (3) STAT674: Applied Data Base Management (3) ELEG633: Image Processing (3) ELEG652: Principles of Parallel Computer Architectures (3) ELEG655: High-Performance Computing with Commodity Hardware (3) ELEG679: Introduction to Medical Imaging Systems (3) ELEG680: Immunology for Engineers (3) CHEG620: Biochemical Engineering (3) CHEG621: Metabolic Engineering (3)

Internship (6) Internship (6) BINF864: Internship (1-6) * Professional Science Master’s Plus Courses – Business/Industry Track † (12) Survey of Business (3) BUAD500: Survey of Business (3) * Leadership and Organization (3)

BUAD870: Leadership and Organizational Behavior (3)

Project Management, Operations or Entrepreneurship (3) [select one]

BUAD831: Operations Management and Management Science (3) BUAD835: Managing New Product Development Projects (3) BUAD871: Managing for Creativity and Innovation (3) ENTR860: High Technology Entrepreneurship (3) MISY840: Project Management and Costing (3)

Intellectual Property (3) CHEG595: Intellectual Property for Engineers and Scientists (3) Professional Science Master’s Plus Courses – Government/Non-Profit Track † (12) Survey of Public Administration(3)

UAPP803: Seminar in Public Administration (3)

Leadership and Organization (3) [select one]

UAPP835: Organization and Management (3)

UAPP604: Leadership in Organizations (3)

Managerial Decision Making or Financial Management (3)

UAPP819: Management Decision Making in Public & Nonprofit Sectors (3)UAPP833: Financial Management in Public & Nonprofit Sectors (3) UAPP827: Program and Project Analysis (3)

7

[select one] UAPP829: Taxation and Fiscal Policies (3) Legal and Regulatory Affairs (3)

UAPP646: Administrative Law and Policy (3)

† Students are recommended to follow one of the tracks, but may cross over tracks to fit interest.

ROUTING AND AUTHORIZATION (Please do not remove supporting documentation.) Department Chairperson Date Dean of College Date Chairperson, College Curriculum Committee___________________________________Date_____________________ Chairperson, Senate Com. on UG or GR Studies Date Chairperson, Senate Coordinating Com. Date Secretary, Faculty Senate Date Date of Senate Resolution Date to be Effective Registrar Program Code Date Vice Provost for Academic Affairs & International Programs Date Provost Date Board of Trustee Notification Date Revised 10/23/2007 /khs

8

APPENDIX - COURSE DESCRIPTIONS BIOINFORMATICS & COMPUTATIONAL BIOLOGY CORE – COMPUTATIONAL

SCIENCES • Bioinformatics

CISC636: Bioinformatics (3) Introduction to concepts, methodologies, and tools in bioinformatics. Abstraction

of biological problems for computational solutions. Genome sequencing and assembly, bio-sequence comparison and database search, dynamics programming, hidden Markov models, and phylogenetic trees. PREREQ: CISC220 or permission of instructor. TERM: Fall Semester

• Introduction to Discipline ELEG671: Introduction to Biomedical Engineering (3)

Mathematical methods in Human Physiology. Introduction to human physiology from a systems perspective, covering all hierarchical levels including molecular, biochemical, cellular, tissue, organ, and integrated systems. Dynamic modeling of physiologic systems including homeostatic control systems, endocrine regulatory systems, immune response dynamics, mutation, selection and evolution. Mathematical methods covered include linear and nonlinear ordinary differential equations, Lyapunov stability analysis, mass action kinetics, Hamming spaces, reaction-diffusion equations, and numerical simulation. TERM: Fall Semester.

BISC602: Molecular Biology of Animal Cells (3) Examination of eucaryotic genes, synthesis and processing of messenger RNA

and control of protein synthesis with emphasis on regulation of normal cellular growth and differentiation and the process of cancer cell transformation. Emphasis on recombinant DNA technology, monoclonal antibody production and tissue culture. PREREQ: BISC401 and BISC403. Requires permission from the instructor. TERM: Fall Semester

BISC612: Advanced Cell Biology (3) Four major sections: (1) cell structure/function; (2) signaling mechanisms and cell

fate; (3) protein biosynthesis and trafficking and (4) integrative cell biology. Requires interpreting and evaluating data from primary scientific literature. Meets literature requirement for biology majors.

BISC654: Biochemical Genetics (3) Covers the use of genetic model organisms to answer biological questions,

including mapping and cloning of human disease genes and the creation of animal models for human genetic diseases. There is an emphasis on examples from the recent scientific literature and building scientific writing skills. PREREQ: BISC403 and BISC401; or permission of instructor

PLSC636: Plant Genes and Genomes (3) Advanced survey of molecular genetics in higher plants, including molecular

methods of plant biotechnology. Topics include genome composition and evolution, transposable elements and retrotransposons, DNA methylation and

9

epigenetics, small RNAs, quantitative traits, chromosome structure and gene expression. PREREQ: PLSC300 and PLSC306.

ANFS670: Principles of Molecular Genetics (3) Fundamentals of nucleic acid biochemistry (replication, repair, and

recombination) and bacterial genetics provide the background needed for detailed study of selected topics in animal and plant molecular biology. PREREQ: ANFS300 or permission of instructor.

MAST616: Methods in Molecular Biology (3) Conceptual experience in molecular biological techniques with an emphasis on

their application to marine related problems. Topics include: nucleic acid extractions, cloning, gene amplification and characterization, and expression methodologies. PREREQ: MAST634

• Systems Biology MATH660: Introduction to Systems Biology (3)

• Systems biology approach, mathematical modeling of biological systems; examples from biomedical and agricultural research areas, biotechnology, industrial processes, and others. Differential equations, stochastic, feedback and control, or network models are discussed. Hands-on work via PBL modules. PREREQ: CHEM527, MATH535 and one of BISC302, 305, 306, 401 or 403.

• Database CISC637: Database Systems (3)

• Physical and logical organization of databases. Data retrieval languages, relational database languages, security and integrity, concurrency, distributed databases. PREREQ: CISC220 and CISC304 or equivalent. TERM: Fall Semester

• Biostatistics STAT613: Multivariate Statistical Methods with Biology Applications (3)

Emphasis on applying multivariate statistical methods in biology. Principal component, factor analysis, discriminant analysis, cluster analysis, and canonical correlation methods are applied for data sets in biology.

STAT656: Biostatistics (3) An introduction to statistics focused toward applications in biological, medical

and other life sciences. Topics include graphical and numerical techniques, random variables and their distribution, estimation and inference. PREREQ: MATH201

ETHICS CORE

BIOL631: Practice of Science (3) Uses historical, philosophical, and sociological perspectives to better understand

the nature of modern science and its practice. Examines "science misconduct," and satisfies the NIH mandate requiring graduate training in "the responsible conduct of research."

UAPP648: Environmental Ethics (3) • Ethical problems associated with environmental protection, local, national, and

international. Relations to social and political movements. Seminar format. UAPP650: Values Ethics and Leadership (3)

10

• Looks at the "ends" served by leaders in various contexts (including government, nonprofits, business, and media) and the ethical standards by which the leaders' actions are judged. Examines cases of unethical conduct as well as cases of exemplary conduct.

BUAD840: Ethical Issues in Global Business Environments (3) • Topics include ethics in organizations, and problems and challenges dealing with

external environment demands including global issues. BIOINFORMATICS & COMPUTATIONAL BIOLOGY INTERNSHIP

BINF864: Internship (1-6) • Supervised, on-the-job experience on specialized topics in bioinformatics or on

industry research and analysis related to bioinformatics. Specialized topics may range from bioinformatics method, tool and database development to the application of bioinformatics approaches to biotechnology and medicine. Industry research and analysis may include topics on product development, project or operations management, and ethical, legal and regulatory affairs.

ELECTIVES – COMPUTATIONAL SCIENCES

CISC841: Algorithms in Bioinformatics (3) Advanced topics in current bioinformatics research, such as hidden Markov

models, kernel based methods, and bayesian based analysis with applications to functional annotation, structural prediction, and biological networks inferences. PREREQ: CISC436 or CISC636 or permission of instructor.

CISC621: Algorithm Design and Analysis (3) Emphasis on developing expertise in the design and analysis of algorithms. Equal

importance given to techniques and specific algorithms. Particular topics include advanced data structures, graph algorithms, disjoint set manipulation, sorting and selection, amortized analysis, NP-completeness, and matrix and polynomial multiplication. PREREQ: Undergraduate algorithms and discrete math courses. TERM: Fall Semester

CISC640: Computer Graphics (3) Computer graphics technology, two- and three-dimensional systems, graphics

software systems, modeling and object hierarchy, and animation. PREREQ: CISC220 or equivalent. COREQ: CISC320 recommended. TERM: Fall Semester

CISC642: Introduction to Computer Vision (3) An introduction to the analysis of images and video to recognize, reconstruct,

model, and otherwise infer static and dynamic properties of objects in the three-dimensional world. Geometry of image formation; image processing such as smoothing, edge and feature detection, color, and texture; segmentation; shape representation including deformable templates; stereo vision; motion estimation and tracking; techniques for 3-D reconstruction; image registration methods. PREREQ: CISC220 equivalent

CISC650: Computer Networks (3)

11

Foundation principles, architectures, and techniques employed in computer and communication networks. Focuses on mechanisms used in TCP/IP protocol suite. Topics include connection management, end-to-end reliable data transfer, sliding window protocols, quality of service, flow control, congestion control, routing, LANs, framing, error control, analog versus digital transmission, packet versus circuit switching, multiplexing. PREREQ: CISC360, CISC361 or CISC663

CISC675: Object Oriented Software Engineering (3) Understand and apply a complete modern software engineering process. Topics

include requirements analysis, specification, design, implementation, verification, and project management. Real-life team projects cover all aspects of software development lifecycle, from requirements to acceptance testing. Use of formal methods in the specification, design, and verification of software will be explored.

CISC681: Artificial Intelligence (3) Programming techniques for problems not amenable to algorithmic solutions.

Problem formulation, search strategies, state spaces, applications of logic, knowledge representation, planning and application areas. PREREQ: CISC220 and CISC304 or equivalent. TERM: Fall Semester

CISC683: Introduction to Data mining (3) Concepts, techniques, and algorithms for mining large data sets to discover

structural patterns that can be used to make subsequent predictions. Emphasis on practical approaches and empirical evaluation. Use of a workbench of data mining tools, such as the Weka toolkit.

CISC882: Natural Language Processing (3) Introduction to computational models of syntax, semantics and pragmatics for

natural language understanding. Emphasis on design of English interfaces to data bases and ill-formed input. PREREQ: CISC681. TERM: Fall Semester

CISC886: Multi-Agent Systems (3) Introduction to the field of Multi-Agent Systems, examining issues that arise

when groups of self-interested or cooperating autonomous agents interact to solve shared problems. Issues include reasoning about the knowledge and beliefs of other agents, communication and negotiation, computational organization, coordination and control. PREREQ: CISC681 or equivalent

CISC887: Internet Information Gathering (3) Approaches to information gathering, filtering, and integration including work in

the heterogeneous database, information retrieval and agent-oriented communities. Text indexing, vector-based and probabilistic retrieval, semantic web technologies, wrappers and mediators, query planning and optimization, collaborative filtering, information agents, applications. PREREQ: CISC681 or equivalent

CISC888: Machine Learning (3) Concepts and algorithms underlying computer programs that learn from data to

solve a task will be discussed. A range of modern machine learning algorithms will be covered.

MATH607: Survey of Scientific Computing (3) Numerical solution of linear systems; interpolation; differentiation and

quadrature; transforms/FFT; nonlinear equations; initial value problems;

12

boundary value problems; Monte Carlo methods; finite difference methods for partial differential equations. Additional topics at the discretion of the instructor. PREREQ: Linear algebra, differential equations, multivariable calculus. TERM: Fall Semester

MATH611: Introduction to Numerical Analysis and Scientific Computing (3) Introduction to numerical computing, analysis and solution of systems of linear

equations, linear least-squares, eigenvalue problems, methods for unconstrained optimization, solution of systems of nonlinear equations. Experience with standard computer packages, code development and simulations of applied problems. PREREQ: Linear algebra and multivariate calculus. TERM: Fall Semester

STAT670: Introduction to Statistical Analysis I (3) Basic probability; continuous, discrete and joint distributions; distribution of

functions of random variables; order statistics; expected value and central limit theorem.

STAT671: Introduction to Statistical Analysis II (3) Distributions of common statistics, sampling techniques, estimation, confidence

intervals, hypotheses testing and selected topics. STAT608: Statistical Research Methods (3)

Experimental design and plot plans, collection, analysis and presentation of data in agricultural and biological research. TERM: Fall Semester

STAT615: Design and Analysis of Experiments (3) Fundamental principles of design, randomized designs, Latin squares, sources of

error, components of error. Factorial designs, response surfaces, models for design. PREREQ: STAT371. TERM: Fall Semester

STAT619: Time Series Analysis (3) Fundamental topics in time series analysis - features the Box and Jenkins

techniques of fitting time series data. Includes an introduction to appropriate statistical packages.

STAT621: Survival Analysis (3) Statistical techniques used in the analysis of censored data including the Kaplan-

Meier estimator, the analysis of one, two and K sample problems, and regression analysis based on the Cox proportional hazards model. RESTRICTIONS: Requires permission of instructor.

STAT674: Applied Data Base Management (3) Provides an in-depth understanding of using computers to manage data using

programs such as SAS and Microsoft/Access. RESTRICTIONS: Requires permission of instructor. TERM: Fall Semester

ELEG633: Image Processing (3) Review of concepts of linear systems and spectral analysis, human visual

response, scanning and display of images, Fourier optics, image enhancement and feature extraction, design of digital filters for image processing, 2D fast Fourier transform algorithms and computed tomography. RESTRICTIONS: Requires permission of instructor. TERM: Spring Semester (may not be offered every year)

ELEG652: Principles of Parallel Computer Architectures (3)

13

Provides an introduction to the principles of parallel computer architecture. Begins at a level that assumes experience in introductory undergraduate courses such as digital system design, computer architecture, and microprocessor based systems. TERM: Spring Semester

ELEG655: High-Performance Computing with Commodity Hardware (3) New commodity computing devices, e.g., GPUs, bring the originally elite high

performance computing into the reach of general public. Principles of program optimization, GPU and IBM Cell architecture, along with concepts and techniques for optimizing general purpose computing on the new hardware. TERM: Fall Semester

ELEG679: Introduction to Medical Imaging Systems (3) Physics, instrumentation, system design, and image reconstruction algorithms will

be covered for the following modalities: radiography, x-ray computed tomography (CT), single photon emission computed tomography (SPECT), positron emission tomography (PET), magnetic resonance imaging (MRI), and real-time ultrasound. RESTRICTIONS: Requires permission of instructor. TERM: Spring Semester

ELEG680: Immunology for Engineers (3) Human adaptive immune response to viruses, both cellular and humoral.

Generation of the immune response cells and response to types of immunogen as well as basic nonlinear differential model analysis, basic mathematical models of their interactions and implications of these models for the treatment of disease. Access significant amount of current literature. No prior knowledge of biology required. RESTRICTIONS: Requires permission of instructor. TERM: Spring Semester (may not be offered every year)

CHEG620: Biochemical Engineering (3) Application of chemical engineering principles to analyze different molecular

engineering approaches, evaluate bioreactors and product recovery processes, analyze cellular engineering approaches and critically evaluate primary bioengineering data from literature and laboratory experiments. PREREQ: MATH243 and CHEM527 or CHEM641 and CHEM642. TERM: Fall Semester

CHEG621: Metabolic Engineering (3) Focuses on design and control of cellular metabolism and includes analysis of

metabolic function using systems engineering and molecular biology tools. Goals are to learn computational approaches for analyzing metabolic behavior, and experimental techniques to measure cellular components, metabolites, proteins and nucleic acids. PREREQ: CHEM527 or CHEM641; MATH305.

PROFESSIONAL SCIENCE MASTER’S PLUS COURSES G.1. BUSINESS/INDUSTRY TRACK

Survey of Business BUAD500: Survey of Business (3)

Survey of business principles including business organization and management, market research and marketing, operations management and decision analysis,

14

accounting and financial analysis. Course assignments stress business technical writing and presentation skills.

Leadership and Organization BUAD870: Understanding People in Organizations (3)

Develops a knowledge base and requisite skills for managing individual, group and organizational processes through the use of diagnostic models, cases and/or experimental experiences.

Project Management, Operations or Entrepreneurship BUAD831: Operations Management and Management Science (3)

Topics include decision analysis tools, mathematical programming, operations strategy, process management and planning and inventory management concepts. PREREQ: BUAD820 or BUAD500

BUAD835: Managing New Product Development Projects (3) Examines techniques and issues in project management, with special emphasis on

new product development projects. Topics include models for cost estimation, process selection, competitive benchmarking, concurrent engineering, and successful project management. Teams prepare proposal for developing and introducing a new product into the marketplace. PREREQ: BUAD831, BUAD880, FINC850 or BUAD500

BUAD871: Managing for Creativity and Innovation (3) Focuses on individual characteristics and group and organizational factors that

influence the ability of organizations to generate new products and/or processes, and to implement new products/processes. Students practice skills to diagnose barriers and develop creative organizations. PREREQ: BUAD870 or BUAD500

ENTR860: High Technology Entrepreneurship (3) Focuses on critical financial, legal, scientific and engineering issues confronted

during initial planning stages of a start-up enterprise. Students work in teams to develop a business plan for a real world business product offering.

MISY840: Project Management and Costing (3) Provides the technical knowledge and skills needed to successfully plan, execute

and evaluate IT projects. Strong emphasis on the costing of IT projects. Intellectual Property

CHEG595: Intellectual Property for Engineers and Scientists (3) Methods of protecting intellectual property. Patents, trademarks, copyrights, trade

secrets and unfair methods of competition, including analyses of significant court decisions in each area. Directed to innovators in all fields interested in legal protection of their ideas.

G.2. GOVERNMENT/NON-PROFIT TRACK

Survey of Public Administration UAPP803: Seminar in Public Administration (3)

Reading and discussion of theories and problems of public administration, including organization, coordination, field administration, contracts, personnel, policy making, participation, adjudication, budgeting and administrative behavior.

15

Leadership and Organization UAPP835: Organization and Management in Public and Nonprofit Sectors (3)

Explores (1) theories and concepts of organizational phenomena, (2) current challenges and implications for the public and nonprofit sectors, and (3) issues for individuals who work in these organizations. Behavioral competencies are developed.

UAPP604: Leadership in Organizations (3) Understanding the process of change and positively affecting change in

organizations through the exercise of leadership skills and knowledge. Managerial Decision Making or Financial Management

UAPP819: Management Decision Making in Public & Nonprofit Sectors (3) Focuses on analytical decision making within public and nonprofit organizations.

Examines processes by which decisions can be made and evaluated. Emphasis on conceptual factors that provide a guide to decisions and evaluations of decision methodologies, e.g., systems analysis, cost-benefit analysis, PERT/critical path method, decision trees, performance measurement and time series.

UAPP833: Financial Management in Public & Nonprofit Sectors (3) Principles of public finance and public sector economics are used to examine

issues of demand for and delivery of public goods by state and local governments and nonprofit organizations. Topics include revenues, expenditures, intergovernmental and cross-sectoral relationships, budgeting, debt management and asset allocation. PREREQ: UAPP834

UAPP827: Program and Project Analysis (3) Explores the ways in which decision-makers in the public sector evaluate the

feasibility of government programs and projects through the application of Cost-Benefit Analysis (CBA), Cost Utility Analysis (CUA), and Cost Effectiveness Analysis (CEA). Focuses on the determination of social costs and social benefits of public policies. PREREQ: UAPP834 or comparable course in public economics and permission of instructor

UAPP829: Taxation and Fiscal Policies (3) Advanced course in theory and application of financing, spending and regulatory

policy instruments of state and local governments. Topics include efficiency, equity and impacts of different types of taxation, user charges, expenditure approaches (transfers/subsidies) and regulation alternatives.

Legal and Regulatory Affairs UAPP646: Administrative Law and Policy (3)

Introduces the basic concepts and rules of administrative law and of the legal issues affecting public and nonprofit organizations in dealing with governmental agencies. Special attention placed on the impact politics has on efforts by administrators to comply with administrative law rules and regulations. No prior legal training or command of legal language necessary.

16

PART II

RESOLUTION STATEMENT

17

PROVISIONAL APPROVAL OF NEW PROGRAMS -- RESOLUTION

PROFESSIONAL SCIENCE MASTER’S IN BIOINFORMATICS COMPUTATIONAL SCIENCES CONCENTRATION

WHEREAS, the proposed Professional Science Master’s degree in Bioinformatics provides a new graduate course of study covering an emerging scientific discipline essential to the 21st century life sciences, the management of the interdisciplinary teams necessary to bring technological advances to the marketplace and the ethical/regulatory issues pertinent to these technological advancements, and

WHEREAS, the proposed Computational Sciences Concentration will allow students to gain solid knowledge and industry experience in developing bioinformatics methods, tools and/or databases for modern biotechnology or medicine, and will prepare them for a bioinformatics professional career in industry, business, government agencies, or non-profit organizations, playing a key role in multi- and interdisciplinary teams, and

WHEREAS, the proposed program builds upon the research strength, education resources and bioinformatics infrastructure from Departments across the Colleges of Arts & Sciences, Engineering, Agriculture & Natural Resources, Earth, Ocean & Environment, Business & Economics, and Education & Public Policy, as well as from the Delaware Biotechnology Institute and the newly established Center for Bioinformatics & Computational Biology, and

WHEREAS, the proposed program contributes to the scholarly and educational missions of the University—to disseminate scientific, humanistic, and social knowledge for the benefit of the larger society and to produce graduates who are prepared to contribute to a global society, addressing the critical needs of the state, nation and global community, and

WHEREAS, the proposed program fosters multi- and interdisciplinary research and educational collaboration across campus, providing a critical component to University’s strategic priorities in energy, environment, and life and health sciences, and serving as a pillar of UD's Path to Prominence, be it therefore RESOLVED, that the Faculty Senate approves provisionally, for five years, the establishment of a new program leading to the Professional Science Master’s degree in Bioinformatics, effective June 1, 2010. RESOLVED, that the Faculty Senate approves provisionally, for five years, the establishment of a new program entitled Professional Science Master’s in Bioinformatics (BINF-PSM), Computational Sciences Concentration (CS1), effective June 1, 2010.

18

PART III

GRADUATE CATALOG

LISTING

19

BIOINFORMATICS & COMPUTATIONAL BIOLOGY Telephone: (302) 831-0161 http://bioinformatics.udel.edu/Education Faculty Listing: http://bioinformatics.udel.edu/Education/faculty A. PROGRAM OVERVIEW Bioinformatics & Computational Biology is an emerging field where biological and computational disciplines converge. The field encompasses the development and application of computational tools and techniques for the collection, analysis, management, and visualization of biological data, as well as modeling and simulation methods for the study of biological systems. Essential to the 21st century life sciences research and key to our understanding of complex biological systems, Bioinformatics & Computational Biology is impacting the science and technology of fields ranging from agricultural, energy and environmental sciences to pharmaceutical and medical sciences. The Professional Science Master’s program in Bioinformatics is administered through the Department of Computer & Information Sciences and coordinated by the Center for Bioinformatics & Computational Biology. The scientific curriculum is supported with the research strength, education resources and bioinformatics infrastructure from ten participating Departments across the Colleges of Arts & Sciences, Engineering, Agriculture & Natural Resources, and Earth, Ocean & Environment, as well as the Delaware Biotechnology Institute. The Computational Sciences Concentration provides knowledge and experience in developing computational methods and bioinformatics tools and databases for modern biological studies, biotechnology or medicine. Graduates of the Professional Science Master’s program will play a key role in multi- and interdisciplinary teams, bridging life sciences and computational sciences. The scientific curriculum, along with “Plus” component for professional skills and the immersive internship will prepare PSM graduates for a professional career in industry or government. B. REQUIREMENTS FOR ADMISSION Admission to the graduate program is competitive. Those who meet stated requirements are not guaranteed admission, nor are those who fail to meet all of those requirements necessarily precluded from admission if they offer other appropriate strengths. The following are the admission requirements to the Professional Science Master’s program in Bioinformatics:

A bachelor’s degree at an accredited four-year college or university with a minimum grade average of 3.0 on a 4.0 system;

20

Applicants may have undergraduate degrees from biological, computational, or other disciplines. However, applicants are expected to have scholarly competence in mathematics, computer science and/or biology;

The following GRE scores are competitive: Quantitative: 650, Verbal + Quantitative: 1200. No GRE subject test is required;

International student applicants must demonstrate a satisfactory level of proficiency in the English language if English is not the first language. The University requires an official paper-based TOEFL score of at least 550, at least 213 on the computer-based TOEFL, or at least 79 on the Internet-based TOEFL. TOEFL scores more than two years old cannot be considered official;

Three letters of recommendation are required. At least one letter must be from professors, other letters can be from employers or others who have had a supervisory relationship with the applicant and are able to assess the applicant’s potential for success in graduate studies; and

Applications must also include a resume outlining work and academic experience, as well as an application essay consisting of the answers to the following questions:

1. What educational background and scientific research or employment experience prepare you for this bioinformatics degree program?

2. What are your long-term professional objectives? 3. What specific attributes of the bioinformatics program make you feel that this

degree is appropriate to help you achieve your professional objectives? C. DEGREE REQUIREMENTS The Professional Science Master’s program in Bioinformatics has the following curriculum requirements:

Science Core in Bioinformatics & Computational Biology (15) Ethics Core (3) Science Electives in Bioinformatics & Computational Biology (6) Internship (6) Professional Science Master’s Plus Courses (12)

o Business/Industry Track (BI) o Government/Non-Profit Track (GN)

The Professional Science Master’s in Bioinformatics requires 24 credits of graduate-level coursework, 6 credits of internship and 12 credits of PSM PLUS coursework, totaling 42 credits. The 24 credits of coursework must include 15 credits in the Bioinformatics & Computational Biology Core courses and 3 credits in the Ethics Core courses. An Internship (BINF864) is required for the PSM degree. The internship will be in most cases completed at participating companies/institutions in the BINF-PSM program and be jointly supervised by the Faculty Advisor and a Co-Mentor in the hosting institution. Unless special permission is granted, students need to complete 12 credit hours prior to the start of their internship. The participating mentors will develop with the internship student specific objectives to be met during the internship, and have the internship approved by the Director of the Master’s

21

BINF-PSM program prior to the start of the internship. A final written report and a poster presentation are required to complete the course. The PSM degree requires at least 12 credits of PLUS coursework in addition to their science core. Whereas students in the PSM program may have professional goals that would lead them into business and industry or to government or non-profit employment, the University of Delaware offers two tracks for the PSM PLUS component. The University recommends the student follow one of the PLUS tracks below, however students may cross over tracks to fit their interest. COMPUTATIONAL SCIENCES CONCENTRATION Credit Requirements: A. Bioinformatics & Computational Biology Core–Computational Sciences………... 15 Credits B. Ethics Core …………………………………………………………………………… 3 Credits C. Electives–Computational Sciences …………………………………………………... 6 Credits D. Internship …………………………………………………………………………..… 6 Credits E. PSM Plus courses…………………………………………………………………..… 12 Credits Total number of required credits: 42 A. Bioinformatics & Computational Biology Core–Computational Sciences (15 credits) Bioinformatics CISC636 Bioinformatics ………………………………………………………………................ 3 Introduction to Discipline (select one) ELEG 671 Introduction to Biomedical Engineering ………………………………………..…… 3 BISC 602 Molecular Biology of Animal Cells ……………………………...…………………… 3 BISC 612 Advanced Cell Biology…………………………………………………………..…… 3 BISC 654 Biochemical Genetics…………………………………………………………..…..… 3 PLSC 636 Plant Genes and Genomes…………………………………………………..…….. 3 ANFS 670 Principles of Molecular Genetics……………………………………………..……… 3 MAST 616 Methods in Molecular Biology………………………………………………..…..… 3 Systems Biology MATH 660 Introduction to Systems Biology………………………………………………….… 3 Database CISC 637 Database Systems………………………………………………………………..….… 3 Biostatistics (select one) STAT 613 Multivariate Statistical Methods with Biology Applications………….………..….… 3 STAT 656 Biostatistics……………………………………………………………………..….… 3 B. Ethics Core (3 credits) Ethics (select one) BIOL 631 Practice of Science………………………………………………………...….………. 3 UAPP 648 Environmental Ethics……………………………………………………..………..… 3 UAPP 650 Values Ethics and Leadership…………………………..………………..….………. 3 BUAD 840 Ethical Issues in Global Business Environments………………………..….………. 3

22

C. Electives–Computational Sciences (6 credits) Electives (select two) CISC 841 Algorithms in Bioinformatics ……………………………………………………….... 3 CISC 621 Algorithm Design and Analysis …………………………………………...….………. 3 CISC 640 Computer Graphics …………………………………………………….……………... 3 CISC 642 Introduction to Computer Vision ….……………………………………….……..…... 3 CISC 650 Computer Networks ………………………………………………………….……..… 3 CISC 675 Object Oriented Software Engineering …………………………...….………………. 3 CISC 681 Artificial Intelligence ……………………………………………...….……………… 3 CISC 683 Introduction to Data mining …………………………………………………………. 3 CISC 882 Natural Language Processing …………………………………………...….………… 3 CISC 886 Multi-Agent Systems ……………………………………………………...….………. 3 CISC 887 Internet Information Gathering …………………………………………...….………. 3 CISC 888 Machine Learning ………………………………………………………...….………. 3 MATH 607 Survey of Scientific Computing ………………………………………...….………. 3 MATH 611 Introduction to Numerical Analysis and Scientific Computing ………….…………. 3 STAT 670 Introduction to Statistical Analysis I ………………………………...….…………….3 STAT 671 Introduction to Statistical Analysis II …………………………………...….……….. 3 STAT 608 Statistical Research Methods ………………………………………...….…………... 3 STAT 615 Design and Analysis of Experiments …………………………………...….………… 3 STAT 619 Time Series Analysis ………………………………………………………...…….… 3 STAT 621 Survival Analysis ………………………………………………………...….………. 3 STAT 674 Applied Data Base Management…………………………………………………….. 3 ELEG 633 Image Processing ………………………………………………………...….………. 3 ELEG 652 Principles of Parallel Computer Architectures ………………………………………. 3 ELEG 655 High-Performance Computing with Commodity Hardware ………………………… 3 ELEG 679 Introduction to Medical Imaging Systems …………………………………………… 3 ELEG 680 Immunology for Engineers ………………………………………………………...… 3 CHEG 620 Biochemical Engineering ………………………………………………………...…. 3 CHEG 621 Metabolic Engineering ………………………………………………………...…….. 3 D. Internship (6 credits) BINF 864 Internship………………………………..……………………………………......… 1-6 E. PSM Plus courses (12 credits) Business/Industry Track Survey of Business BUAD 500 Survey of Business ……………………………….…………………………...…….. 3 Leadership and Organization BUAD 870 Understanding People in Organizations ……………………………………………. 3 Project Management, Operations or Entrepreneurship (select one) BUAD 831 Operations Management and Management Science ……………………………….. 3 BUAD 835 Managing New Product Development Projects ……………………………………. 3 BUAD 871 Managing for Creativity and Innovation ………………………………………..….. 3 ENTR 860 High Technology Entrepreneurship ………………………………………………..... 3 MISY 840 Project Management and Costing …………………………………………………… 3 Intellectual Property

23

CHEG 595 Intellectual Property for Engineers and Scientists …………………………...…….. 3

Or Government/Non-Profit Track Survey of Public Administration UAPP 803 Seminar in Public Administration …………………………..………………...…….. 3 Leadership and Organization (select one) UAPP 835 Organization and Management in Public and Nonprofit Sectors ……………...…….. 3 UAPP 604 Leadership in Organizations …………………………………………………...…….. 3 Managerial Decision Making or Financial Management (select one) UAPP 819 Management Decision Making in Public & Nonprofit Sectors ……………….…….. 3 UAPP 833 Financial Management in Public & Nonprofit Sectors …………………...…...…….. 3 UAPP 827 Program and Project Analysis ………………………………………………...…….. 3 UAPP 829 Taxation and Fiscal Policies …………………………………………………...…….. 3 Legal and Regulatory Affairs UAPP 646 Administrative Law and Policy ……………………………………………………… 3

24

PART IV

PROPOSAL

25

I. DESCRIPTION The completion of the human genome sequence marked the beginning of a new era of biological research. Scientists have begun to systematically tackle gene functions and other complex regulatory processes by studying organisms at the global scales. Advances in high-throughput biotechnologies and large-scale bioscience have further enabled modeling and simulation over a multitude of length, time and biological scales from biomolecules, cells, tissues and organs to organisms and population. With the enormous volume of data being produced, biology is becoming an increasingly quantitative science. Computational approaches, in combination with experimental methods, have become essential for generating novel hypotheses, deriving new scientific knowledge, and driving discovery and innovation. Bioinformatics & Computational Biology is an emerging field where biological and computational disciplines converge. According to the National Institutes of Health, the working definitions of Bioinformatics and Computational Biology are as follows:

Bioinformatics: Research, development, or application of computational tools and approaches for expanding the use of biological, medical, behavioral or health data, including those to acquire, store, organize, archive, analyze, or visualize such data.

Computational Biology: The development and application of data-analytical and theoretical methods, mathematical modeling and computational simulation techniques to the study of biological, behavioral, and social systems.

Fundamental to the modern day biological studies and key to the basic understanding of complex biological systems, Bioinformatics & Computational Biology is impacting the science and technology of fields ranging from agricultural and environmental sciences to pharmaceutical and medical sciences. The research requires close collaboration among multi-disciplinary teams of researchers in quantitative sciences, life sciences, and their interfaces. The Professional Science Master’s program in Bioinformatics aims to train the next-generation of researchers and professionals who will play a key role in multi- and interdisciplinary teams, bridging life sciences and computational sciences. The program will be administered through its academic home, the Department of Computer & Information Sciences, and will be coordinated by the newly established Center for Bioinformatics & Computational Biology. The scientific curriculum will build upon the research and educational strength from departments across the Colleges of Arts & Sciences, Engineering, Agriculture & Natural Resources, and Earth, Ocean & Environment. The program will be synergistic to the existing degree programs, providing a critical component to University’s strategic priorities in energy, environment, and life and health sciences, and serving as a pillar of UD's Path to Prominence.

II. RATIONALE AND DEMAND

The University of Delaware currently does not offer a specialized graduate degree in Bioinformatics & Computational Biology, although related courses have been taught in several departments for a number of years. We propose to develop a Professional Science Master’s program in Bioinformatics. The rationales are:

26

Bioinformatics & Computational Biology is essential to 21st century life science research

in academia and industry; The program will build upon the research strength and bioinformatics infrastructure at the

Delaware Biotechnology Institute and from departments across the Colleges of Arts & Sciences, Engineering, Agriculture & Natural Resources, and Earth, Ocean & Environment;

The program will offer graduate education in a discipline essential for UD as a major research university, providing a critical component to University’s strategic priorities in energy, environment, and life and health sciences. Indeed the program aligns with the University strategic plan to “engage closely with the critical issues of our day, to increase the global impact of the University, and to raise its prominence in the world.”

The Professional Science Master’s in Bioinformatics (BINF-PSM) will position UD as a regional leader in bioinformatics professional education. The scientific curriculum, together with “Plus” component for professional skills and the immersive Internship will well prepare the BINF-PSM graduates to pursue a career in industry, business, government agencies, or non-profit organizations. The Computational Sciences Concentration (CS1) will allow students with strong quantitative sciences background to gain solid knowledge and industry experience in developing bioinformatics methods, tools and/or databases for modern biotechnology or medicine.

A. INSTITUTIONAL FACTORS A.1. COMPATIBILITY WITH UNIVERSITY ACADEMIC PRIORITIES A strong educational program in Bioinformatics & Computational Biology will contribute to the scholarly and educational missions of the University—to disseminate scientific, humanistic, and social knowledge for the benefit of the larger society and to produce graduates who are prepared to contribute to a global society, addressing the critical needs of the state, nation and global community. A.2. PLANNING PROCESS The planning process started in Spring 2009 after the recruitment of Dr. Cathy H. Wu, Edward G. Jefferson Professor of Bioinformatics & Computational Biology, who was charged to take the responsibility and leadership for establishing the Center for Bioinformatics & Computational Biology at the University of Delaware and the development of new graduate programs in Bioinformatics & Computational Biology. A Bioinformatics Steering Committee was established in June 2009 to guide the development of the Master’s program in Bioinformatics & Computational Biology. The committee consists of faculty members from ten Departments across four Colleges participating in this degree program, with expertise in areas ranging from genomics and systems biology to biostatistics and high performance computing (Table 1). The committee meets monthly throughout the entire planning process to discuss all aspects of the program development.

27

Table 1. Bioinformatics Steering Committee Member College Department Expertise

Wu, Cathy (Chair) Arts & Sciences Computer & Information Sciences

Bioinformatics and Computational Biology

Antoniewicz, Maciek Engineering Chemical Engineering Metabolic Engineering, Systems Biology

Bahnson, Brian Arts & Sciences Chemistry & Biochemistry

Structure Biology, Molecular Modeling

Duncan, Melinda Arts & Sciences Biological Sciences Biotechnology PSM, Developmental Biology

Hanson, Thomas Earth, Ocean & Environment

Marine Biosciences Microbial Genomics

Lee, Kelvin Engineering Chemical Engineering Systems Biology, Proteomics

Liao, Li Arts & Sciences Computer & Information Sciences


Marsh, Adam Earth, Ocean & Environment

Marine Biosciences Environmental Bioinformatics

Meyers, Blake Agriculture & Natural Resources

Plant & Soil Sciences Plant Genomics, Bioinformatics

Rejto, Lidia Agriculture & Natural Resources

Food & Resource Economics

Biostatistics

Schleiniger, Gilberto Arts & Sciences Mathematical SciencesQuantitative Biology BS Major, Mathematical Biology

Schmidt, Carl Agriculture & Natural Resources

Animal & Food Sciences

Avian Genomics

Taufer, Michaela Arts & Sciences Computer & Information Sciences

Grid Computing, Cloud Computing

Wommack, Eric Agriculture & Natural Resources

Plant & Soil Sciences Viral Genomics

Zurakowski, Ryan Engineering Electrical & Computer Engineering

Biomedical Engineering

Meanwhile, Dr. John Sawyer, Director of Professional Education Initiatives, Office of the Vice Provost for Graduate and Professional Education, has coordinated the development of the PSM programs on campus, and in particular, spearheaded the development of the “Plus” component. The initial effort has focused on the Biotechnology PSM (to be directed by Dr. Melinda Duncan, Graduate Program Director, Department of Biological Sciences) and the Bioinformatics PSM (to be directed by Dr. Cathy Wu). A key aspect of the PSM program development is to interact with the regional Biosciences industry to collaboratively define attributes of the course curriculum that are highly compatible to industry needs, and to detail the education benefits available to the employees in the participating organizations. A Bioinformatics Industry Advisory Board was established in July 2009 to advise the development of the Master’s program in Bioinformatics & Computational Biology from industry

28

perspectives. The Board consists of representatives from major regional companies and institutions who have committed to host internships (Table 2).

Table 2. Bioinformatics Industry Advisory Board Member Title Organization Tomb, Jean-Francois (Chair)

Manager – Bioinformatics at DuPont DuPont Central Research & Development

Barbara, Deb VP, New Business Development Strategic Diagnostics, Inc.

Bunnell, Tim Director, Center for Pediatric Auditory & Speech Sciences

duPont Hospital for Children

Christianson, Anastasia

Director of Discovery Medicine Informatics

AstraZeneca

Foutrakis, George Associate, GORE Medical Products W.L. Gore Hollis, Greg VP, Applied Technology Group Incyte

Weintraub, William Director, Christiana Center for Outcomes Research

Christiana Care

Wright, Ian Head of Global Assay Development Siemens Healthcare Diagnostics The Bioinformatics Graduate Committee was established in August 2009 to be responsible for the admission, advising, and progress assessment of the students in the Master’s program in Bioinformatics & Computational Biology. The committee consists of at least two representative faculty members from each participating College in this degree program (Table 3).

Table 3. Bioinformatics Graduate Committee Member College Department

Wu, Cathy (Chair) Arts & Sciences Computer & Information Sciences/ Biological Science

Hanson, Thomas Earth, Ocean & Environment Marine Biosciences Lee, Kelvin Engineering Chemical Engineering Liao, Li Arts & Sciences Computer & Information Sciences Papoutsakis, Eleftherios Engineering Chemical Engineering Patel, Sandeep Arts & Sciences Chemistry & Biochemistry Rejto, Lidia Agriculture & Natural Resources Food & Resource Economics Schleiniger, Gilberto Arts & Sciences Mathematical Sciences Schmidt, Carl Agriculture & Natural Resources Animal & Food Sciences

Wommack, Eric Agriculture & Natural Resources/ Earth, Ocean & Environment

Plant and Soil Sciences/ Marine Biosciences

A.3. SIGNIFICANT IMPACT ON OTHER UNIVERSITY PROGRAMS The positive impact of the proposed Professional Science Master’s program in Bioinformatics on University research and educational programs is multi-fold:

It will offer graduate education in a discipline essential for University of Delaware as a major research university. According to the listing at the International Society for

29

Computational Biology web site (http://www.iscb.org/iscb-degree-certificate-programs), there are presently 180 bioinformatics-related degree programs worldwide, almost 100 in the United States alone;

It will provide courses that can be used as electives in current graduate and undergraduate degree programs, and used for the development of new minors, concentrations, or degree programs, thus, complementing, not competing with already existing degree programs;

It will create a context for faculty from the various participating disciplines across-campus to articulate the interface of their research and foster research collaborations;

It will produce graduate students with knowledge and professional expertise in bioinformatics and computational biology, who can play a key role in multi- and interdisciplinary teams;

The educational program, coupling with collaborative interdisciplinary research, will provide a solid foundation for University of Delaware to compete for training grants (such as NSF’s IGERT-Integrative Graduate Education and Research Traineeship Program and NIH’s Institutional Research Training Grants) and research grants (such as NIH’s CTSA-Clinical and Translational Science Award);

The educational program will provide a solid foundation for the future development of a PhD degree program in Bioinformatics & Computational Systems Biology (planned for Fall 2012 start);

As a supplementary benefit, offering the Professional Science Master’s potentially represents a source of income for the University.

A.4. UTILIZATION OF EXISTING RESOURCES With strong computational and engineering programs and full biological disciplines from health sciences to agriculture and marine studies, as well as state-of-the-art facilities for bioinformatics at the Delaware Biotechnology Institute, the University of Delaware provides a rich environment for educational programs in Bioinformatics & Computational Biology. The proposed curricula fully leverage the course offerings from the following departments/units across Colleges. The letters of approval from contributing department/units are attached in Appendix I. B. STUDENT DEMAND According to many accredited scientific and industry reviews, bioinformatics and computational biology may well be the single fastest-growing specialty in the life sciences. A recent report estimates the current global bioinformatics market at about $1.4 billion, and is projecting an average annual growth rate of 15.8 per cent to reach nearly $3 billion by 2010, reflecting bioinformatics' explosive growth. The Professional Science Master’s Program has evolved over the last decade across the USA. A report from the National Academies said, “The time is right to accelerate and spread nationally the development of professional science master’s degrees that are interdisciplinary in character, strongly emphasize effective communication and problem solving, and provide an understanding of entrepreneurial skills and technical innovation.” The National Research Council recognizes PSM degree programs as uniquely promising for preparing bioscience talent.

30

B.1. ENROLLMENT PROJECTIONS We project that we will have a steady increase in new students entering the Professional Science Master’s program in Bioinformatics each year and reach 5 new students in the steady state. The projection is based on a M.S. Bioinformatics Track program established by Wu at Georgetown University, where enrollment has increased steadily each semester since its launching in Fall 2009. Based on the enrollment of similar programs, we project that 50% of BINF-PSM students will be full-time. Full-time student is expected to complete the BINF-PSM program (42 credits) in two years. The program may be completed over a longer time frame for part-time students. B.2. NEEDS OF STUDENT CLIENTELES The Professional Science Master’s program in Bioinformatics will support students from different educational backgrounds and with different career aspirations, while leveraging the common course curriculum. The students, full-time or part-time, may come from various backgrounds, or even from “unconventional” fields such as business, management, law and medicine. They may be interested in applying bioinformatics as an integral approach to life science research and development, or interested in developing new computational methods and bioinformatics tools and databases. Graduates of this program will leave well prepared to pursue careers in business, industry, government agencies, or non-profit organizations.

C. TRANSFERABILITY Prior to admission to the Professional Science Master’s program in Bioinformatics, a prospective student from another institution can be approved by the Graduate Committee to take up to 9 graduate credits that, if/when admitted to the degree program, would be applied to that degree. Graduate courses counted toward a degree received elsewhere may not be transferred into a degree at the University of Delaware. Once the student has successfully completed 9 approved graduate UD credits and been admitted to the degree program, then a maximum of 9 graduate credits can be transferred into the Master’s program from another institution with the approval of the Graduate Committee. Students who complete graduate credits with the classification of CEND (Continuing Education Non-degree) at the University of Delaware may use a maximum of 9 graduate credits earned with this classification toward their graduate degree. Students matriculated in other graduate degree programs upon admission to the Professional Science Master’s program in Bioinformatics may transfer their graduate credits provided that: (i) the course was at the 600-800 level, (ii) the course was taken within the time limit appropriate for the degree, and (iii) the course was approved by the Graduate Committee and in accordance with the student's plan of study.

D. ACCESS TO GRADUATE AND PROFESSIONAL PROGRAMS

31

The graduates of the Professional Science Master’s program in will have different career paths. And may consider the program as a terminal degree.

E. DEMAND AND EMPLOYMENT FACTORS The demand and growth of bioinformatics and computational biology as a research field and in the global industry have been discussed above (sections I and II.B). Our close collaboration with the regional Biosciences industry will provide opportunities for industry internship, career advising, as well as employment opportunities.

F. REGIONAL, STATE AND NATIONAL FACTORS According to the listing at the International Society for Computational Biology web site, there are presently 180 bioinformatics-related degree programs worldwide, almost 100 in the United States alone. F.1. COMPARABLE COURSES OF STUDY IN THE REGION OR STATE No other university in the State of Delaware offers a Professional Science Master’s program in Bioinformatics & Computational Biology. In the Delaware Valley region, there are only two graduate degree programs in Bioinformatics & Computational Biology, an interdisciplinary Ph.D. program in Genomics and Computational Biology at the University of Pennsylvania, and a Master’s (non-thesis M.S.) in Bioinformatics at the University of the Sciences in Philadelphia. We believe that the UD Professional Science Master’s program in will emerge as a highly competitive educational opportunity based on: (i) a strong scientific core curriculum and comprehensive list of elective courses with many subfields in Computational Sciences, (ii) proximity to major biotech and pharmaceutical industry and active participation of regional industry partners, (iii) rich opportunities for immersive internships, and (iv) the competitive total cost of the degree program. F.2. EXTERNAL REQUIREMENTS We note that there are no formal guidelines for a Professional Science Master’s program in Bioinformatics, nor are there accreditation standards. The proposed curriculum was designed based on a careful study of bioinformatics and computational biology curricula offered by other institutions. We have closely examined offered programs at selected, prominent research universities, conducted a series of talks with the local industry partners, and recognized the needs from both the student and employer perspectives. The proposed curriculum compiles the information gathered from these resources into one carefully tailored program.

G. OTHER STRENGTHS G.1. SPECIAL FEATURES

32

A special feature of the proposed program is the close collaboration among participating Departments across Colleges. These departments are working together to develop and offer courses for this new Professional Science Master’s program in Bioinformatics. Going forward, this collaboration will continue in the form of the Bioinformatics Steering Committee and the Bioinformatics Graduate Committee. Another feature of the program is its coordination through the Center for Bioinformatics & Computational Biology, which provides extensive bioinformatics resources and capabilities at the BioIT Center at the Delaware Biotechnology Institute (DBI) and the Protein Information Resource (PIR). The BioIT Center provides both computing infrastructure and cyber-knowledgeable personnel with significant hardware, software and professional support for computational and data management needs. The computing infrastructure includes a High-Performance Compute Cluster, a Database Server Cluster, and an immersive 3-D Visualization Studio. The PIR is a public bioinformatics resource that provides integrated databases and analytical tools to support genomics, proteomics and systems biology research. The PIR web sites are freely accessible by researchers worldwide with over 4 million hits per month from over 100,000 unique sites, while the FTP sites serve over 1 terabyte of data download monthly. G.2. COLLABORATIVE ARRANGEMENTS No collaborative arrangement is required.

III. ENROLLMENT, ADMISSIONS AND FINANCIAL AID A. ENROLLMENT There is no need to limit enrollment due to resources. Enrollment is estimated at 20 new students per academic year in the steady state. Based on the entrance requirements and specified prerequisites, students may enroll in the Master’s program with a regular status or provisional status:

Regular status is offered to students who meet all of the established entrance requirements, who have a record of high scholarship in their fields of specialization, and who have the ability, interest, and maturity necessary for successful study at the graduate level in a degree program.

Provisional status is offered to students who are seeking admission to the degree program but lack one or more of the specified prerequisites. All provisional requirements must be met within the deadline given before regular status can be granted. Students admitted with provisional status are generally not eligible for assistantships or fellowships. Students who file an application during the final year of undergraduate or current graduate work and are unable to supply complete official transcripts showing the conferral of the degree will be admitted pending conferral of the degree if their records are otherwise satisfactory and complete. For students lacking appropriate preparatory course work, additional courses applicable to certain areas of study may be required prior

33

to admission or students may be admitted with the provision that completion of certain area content courses be completed concurrent with the courses in the degree program.

B. ADMISSION REQUIREMENTS B.1. SELECTION CRITERIA Admission to the graduate program is competitive. Those who meet stated requirements are not guaranteed admission, nor are those who fail to meet all of those requirements necessarily precluded from admission if they offer other appropriate strengths. The following are the admission requirements to the Professional Sciences Master’s program in Bioinformatics:




International student applicants must demonstrate a satisfactory level of proficiency in the English language if English is not the first language. The University requires an official TOEFL score of at least 550 on paper-based, 213 on computer-based, or 79 on Internet-based tests. TOEFL scores more than two years old cannot be considered official. Alternatively, IELTS can be accepted in place of the TOEFL. The minimum IELTS score is 6.5 overall with no individual sub-score below 6.0.


Applications must also include a resume outlining work and academic experience, as well as an application essay consisting of the answers to the following questions: 1. What educational background and scientific research or employment experience

prepare you for this bioinformatics degree program? 2. What are your long-term professional objectives? 3. What specific attributes of the bioinformatics program make you feel that this degree

is appropriate to help you achieve your professional objectives? B.2. CHANGE OF CLASSIFICATION Students currently matriculated in other graduate degree programs should complete a “Change of Classification Form” to seek approval to enter the Professional Science Master’s program in Bioinformatics & Computational Biology. The Bioinformatics Graduate Committee will evaluate each “Change of Classification” request on a case-by-case basis and determine whether the

34

student is required to submit a completed admission application form to the Office of Graduate and Professional Education and follow the same procedures for admission as other applicants. Students should also complete a “Change of Classification Form” for moving within the Master’s program in Bioinformatics and Computational Biology, e.g., from BINF-CERT to BICB-MS or BINF-PSM; or from BICB-MS to BINF-PSM. The Bioinformatics Graduate Committee will evaluate and approve the transfer requests on a case-by-case basis. A student in the BICB-MS program who has been funded on a Graduate Assistantship will require the consent of the Faculty Advisor for transfer to another degree option in the program. B.3. APPLICATION DEADLINES Admission decisions are made on a rolling basis as and when applications are complete. The application deadlines are:

Fall Semester: July 1st (regular application); March 1st (financial aid) Spring Semester: December 1st (regular application); October 1st (financial aid)

C. STUDENT EXPENSES AND FINANCIAL AID C.1. STUDENT EXPENSES The Professional Science Master’s program in Bioinformatics does not require student expenses beyond the traditional book and supplies, except for the availability of a personal computer or laptop. C.2. FINANCIAL AID Admission to the Professional Science Master’s program in Bioinformatics does not automatically entitle an applicant to financial aid. Students may seek financial aid opportunities, such as fellowships or scholarships from sources within the University and from private and federal agencies. Interested students should check the Office of Graduate Studies for the most current opportunities. Financial aid is awarded on a competitive basis from the pool of admitted applicants. The University of Delaware's policies apply to all forms of financial aid. Please refer to the University Policies for Graduate Student Assistantships and Fellowships. Students in the Professional Science Master’s program may apply for Industry Internships. Paid internships may be available from industry, government agencies or other participating institutions in the Master’s program in Bioinformatics.

IV. CURRICULUM SPECIFICS

A. INSTITUTIONAL FACTORS

35

Students who successfully complete the program will be awarded the following degree: Professional Science Master’s in Bioinformatics (BINF-PSM).

B. CURRICULUM DESCRIPTION B.1. DEGREE REQUIREMENTS


15 Credits


12 Credits

B.2. CURRICULUM The tables below list the course curriculum for the major components of the Professional Science Master’s program in Bioinformatics. New or revised courses required for the curriculum are marked. All of these courses have been submitted to the Course Challenge list and will be effective for the Fall 2010 term. Bioinformatics & Computational Biology Core – Computational Sciences (15) Bioinformatics (3) CISC636: Bioinformatics (3) *





CISC636: Bioinformatics (3) * submitted for re-title from “Introduction to Bioinformatics” PLSC636: Plant Genes and Genomes (3) * submitted for re-title from “Advanced Plant Genetics” MATH660: Introduction to Systems Biology (3) * adapted from MATH460 STAT613: Multivariate Statistical Methods with Biology Applications (3) * new course being developed

Ethics Core (3)


BISC631: Practice of Science (3) UAPP648: Environmental Ethics (3) UAPP650: Values Ethics and Leadership (3)

36

BUAD840: Ethical Issues in Global Business Environments (3) Internship (6) Internship (6) BINF864: Internship (1-6) *

BINF864: Internship * new course listing Electives – Computational Sciences (6)

Electives (6) [select two]

CISC841: Algorithms in Bioinformatics (3) CISC621: Algorithm Design and Analysis (3) CISC640: Computer Graphics (3) CISC642: Introduction to Computer Vision (3) CISC650: Computer Networks (3) CISC675: Object Oriented Software Engineering (3) CISC681: Artificial Intelligence (3) CISC683: Introduction to Data mining (3) CISC882: Natural Language Processing (3) CISC886: Multi-Agent Systems (3) CISC887: Internet Information Gathering (3) CISC888: Machine Learning (3) MATH607: Survey of Scientific Computing (3) MATH611: Introduction to Numerical Analysis and Scientific Computing (3)STAT670: Introduction to Statistical Analysis I (3) * STAT671: Introduction to Statistical Analysis II (3) * STAT608: Statistical Research Methods (3) STAT615: Design and Analysis of Experiments (3) STAT619: Time Series Analysis (3) STAT621: Survival analysis (3) STAT674: Applied Data Base Management (3) ELEG633: Image Processing (3) ELEG652: Principles of Parallel Computer Architectures (3) ELEG655: High-Performance Computing with Commodity Hardware (3) ELEG679: Introduction to Medical Imaging Systems (3) ELEG680: Immunology for Engineers (3) CHEG620: Biochemical Engineering (3) CHEG621: Metabolic Engineering (3)

STAT670: Introduction to Statistical Analysis I (3) * new course being developed STAT671: Introduction to Statistical Analysis II (3) * new course being developed

Professional Science Master’s Plus Courses – Business/Industry Track † (12) Survey of Business (3) BUAD500: Survey of Business (3) * Leadership and Organization (3)




37






Managerial Decision Making or Financial Management (3) [select one]

UAPP819: Management Decision Making in Public & Nonprofit Sectors (3)UAPP833: Financial Management in Public & Nonprofit Sectors (3) UAPP827: Program and Project Analysis (3) UAPP829: Taxation and Fiscal Policies (3)

Legal and Regulatory Affairs (3)

UAPP646: Administrative Law and Policy (3)

BUAD500: Survey of Business (3) * new course being developed † Students are recommended to follow one of the tracks, but may cross over tracks to fit interest.

V. RESOURCES AVAILABLE

A. LEARNING RESOURCES There are no special Learning Resources required to support this degree program. No new library or technology resources will be required for this Professional Science Master’s program in Bioinformatics, as it will extend from the previous courses in the participating departments and build upon the bioinformatics infrastructure at the Delaware Biotechnology Institute. The library's current holdings and subscriptions have covered major bioinformatics journals (many are open-access) and are sufficient as instructional materials.

B. FACULTY/ADMINISTRATIVE RESOURCES Faculty resources will be available to the Professional Science Master’s program in Bioinformatics for course offerings from the participating departments. Faculty members may serve as course directors, course instructors, and/or research mentors. The research mentors will also serve as the Faculty Advisor who will be the primary contact for students and will develop a course of study with the student before the beginning of the second semester. All the courses in the curriculum will be offered every year, except for a few elective courses, which may be offered every other year. The total enrollment each year from the Professional Sciences Master’s program is projected at 5 students in the steady state. The demand from Bioinformatics & Computational Biology students can be absorbed by most existing classes. In a few cases, especially for the Core courses (such as CISC637 Database Systems), additional sections may be needed. Additional faculty and administrative resources will be available from the Center for Bioinformatics & Computational Biology. These include: (i) four tenure-track faculty positions for faculty recruitment in critical areas of bioinformatics research and education–a search is

38

currently underway for one position in the College of Arts & Sciences, (ii) an Administrative Assistant for administrative assistance for three years, and (iii) bioinformatics research faculty and scientific staff at the BioIT Center and PIR at Delaware Biotechnology Institute.

C. EXTERNAL FUNDING Unidel Foundation funds have been requested to support a Scientific Coordinator position for three years at the Center for Bioinformatics & Computational Biology. The Coordinator will be recruited at the rank of Research Assistant Professor to assist the Center Director in managing and coordinating activities in all three areas of research, education and core. If funded, the Coordinator will provide day-to-day management of the Master’s program in Bioinformatics & Computational Biology and assist with student recruitment, admission, advising, progress assessment, and career planning. In addition, funds were requested to support Center activities including seminar series, training workshops and research symposiums. This will provide support for the Bioinformatics Seminar course (BINF865) and for an annual Research Day at the University of Delaware where PSM students will present posters and showcase their internship projects.

VI. RESOURCES REQUIRED

A. LEARNING RESOURCES Students in the program will utilize standard University computing systems. No new learning resources are required.

B. PERSONNEL RESOURCES No additional personnel resources will be requested beyond the faculty and administrative resources described in Section V.

C. BUDGETARY NEEDS C.1. PROJECTED EXPENSES The projected expenses for the Professional Science Master’s program in Bioinformatics include personnel costs for program administration, course instruction, mentoring and student scholarships, as well as costs for advertisement, materials and supplies and for hosting program activities. % Effort/Costs Initial Funding

Personnel Expenses

39

Program Administration

Faculty Director 3.3% Arts & Sciences (CBCB) Program Coordinator (Research Faculty) 10.0% Unidel (CBCB) Administrative Assistant 6.7% Arts & Sciences (CBCB) Administration Personnel Total 0.2 FTE Course Instruction, Mentoring, Fellowships Additional Sections of Existing Courses 12.5%/course Participating Departments/Colleges New Course Development 12.5%/course Participating Departments/Colleges Student Scholarships 50% tuition Participating Departments/Colleges Operational Expenses Web Design and Maintenance $1,700 Arts & Sciences (CBCB) Brochures and Advertisement $6,700 Arts & Sciences (CBCB) Materials and Supplies $3,300 Arts & Sciences (CBCB) Bioinformatics Seminars and Research Day $3,300 Unidel (CBCB) Operational Expenses Total $15,000

* Covers both Computational Sciences Concentration and Life Sciences Concentration. The initial funding for the administration personnel costs is available from the College of Arts & Sciences (and from the Unidel Foundation if funded) through the Center for Bioinformatics & Computational Biology (CBCB). The costs for course instruction by tenure-track faculty represent redirections of effort, as their salaries are already being paid by the respective Departments/Colleges. There may be needs to establish S-Contracts for part-time instructors to offer new sections of existing courses or to develop new courses in the future, especially for researchers or professionals from the collaborating companies and institutions who may provide industry perspectives and real-world problem-based learning. The Bioinformatics Steering Committee further recommends that financial assistance be sought from Deans of the participating Colleges to provide tuition recovery for Professional Science Master’s Faculty Advisors who will serve as faculty co-mentor of industry internship and will be responsible for supervising the PSM students throughout their entire course of study. Other operational expenses for the Professional Science Master’s program include recurring annual costs for recruitment and marketing, materials and supplies, and educational program activities. The latter will include honorarium and travel supports for invited speakers participating in the Research Day, as well as costs for hosting the Research Day events and student poster presentations. C.2. BUDGET PLAN The tuition income constitutes the major income for the Professional Science Master’s program in Bioinformatics. Based on the assumption that we will have a steady increase in new enrollment of full-time student equivalents (FTEs) from two students in year one to five students in year four when it reaches a steady state, the program is likely to have a net income starting the third year. The table below provides the projection of the number of new admits each year and the total number of students of the two-year program.

40

Student Enrollment (New/Total FTEs) Y01 Y02 Y03 Y04 Y05Professional Science Master (PSM) 2/2 3/5 5/8 5/10 5/10

A budget plan should be in place and agreed upon among the Deans of the participating Colleges to cover the costs of launching the program initially, to incentivize faculty members to participate and contribute to this educational program, and to share the profit generated by the success of the program. The proposed Professional Science Master’s program in Bioinformatics is fully endorsed by the Deans of the following participating Colleges. Their letters of support are attached in Appendix II.

College of Arts & Sciences: College of Agriculture & Natural Resources College of Engineering College of Earth, Ocean & Environment

VII. IMPLEMENTATION AND EVALUATION

A. IMPLEMENTATION PLAN The Professional Science Master’s program in Bioinformatics is planned for an official start in the Fall semester of 2010. The Bioinformatics Graduate Committee will establish policies of their operation and for the program, and coordinate with the home department and other participating departments about course offerings. Simultaneously with this proposal, Faculty Senate approval will be sought for new or revised courses required for the curriculum, as submitted to the Course Challenge list. B. ASSESSMENT PLAN B.1. PROGRAM OBJECTIVE The Professional Science Master’s program in Bioinformatics aims to train the next-generation of researchers and professionals who will play a key role in multi- and interdisciplinary teams, bridging life sciences and computational sciences. The Professional Science Master’s degree will well prepare students for a bioinformatics professional career in industry, business, government agencies, or non-profit organizations. B.2. CURRICULAR MAP AND LEARNING OUTCOMES The Professional Science Master’s program has five major curriculum components:

1. Science Core in Bioinformatics & Computational Biology 2. Ethics Core 3. Science Electives in Bioinformatics & Computational Biology

41

4. Internship in Bioinformatics & Computational Biology 5. Professional Science Master’s Plus Courses

The curricular map indicates the following learning outcomes addressed in the curriculum:

1. Core competency in bioinformatics & computational biology 2. Knowledge of scientific/business ethics 3. Advanced knowledge of bioinformatics & computational biology and related disciplines 4. Independent mentored research experience in bioinformatics & computational biology 5. Working experience of bioinformatics in industry and business 6. Competence in scientific communication 7. Experience working with interdisciplinary teams, bridging life sciences and

computational sciences 8. Professional knowledge and skills in business or public administration, leadership and

organization, project management, and legal and regulatory affairs

Learning Outcomes

Curriculum

Cor

e co

mpe

tenc

y in

Bio

info

rmat

ics

Kno

wle

dge

of e

thic

s

Adv

ance

d kn

owle

dge

of

bioi

nfor

mat

ics

& r

elat

ed d

isci

plin

es

Inde

pend

ent r

esea

rch

expe

rien

ce

Wor

king

exp

erie

nce

of

bioi

nfor

mat

ics

in in

dust

ry

Com

pete

nce

in s

cien

tifi

c co

mm

unic

atio

n

Exp

erie

nce

wor

king

wit

h in

terd

isci

plin

ary

team

s

Pro

fess

iona

l kno

wle

dge

and

skil

ls

Science Core x Ethics Core x Science Electives x Internship x x x x PSM Plus x

B.3. ASSESSMENT PLAN

Objectives Strategic Activities

Measures Short-term Outcomes

Long-term Impact

42

Train students in the science disciplines pertinent to bioinformatics & computational biology

Recruit excellent applicant and matriculate students with credentials similar to those in UD graduate programs

Number and demographic data of student applicants and matriculated students

Retention and time to degree statistics

Students gain employment in bioinformatics related fields

Course work covering the disciplines related to bioinformatics & computational biology (Science Core and Electives)

Faculty evaluation of student progress in course work;

Survey of faculty advisors and internship mentor;

Surveys of graduate students in the program and post-graduation

Course work helped students secure initial employment;

Students and graduates report applying knowledge from courses to work settings

Graduates enjoy long term success in academic or professional careers

Provide training in science-related ethics, business, organizational management, project management, legal and regulatory affairs

Course work addressing these issues and industry internship experience (Ethics Core and PSM Plus)

Surveys of students focusing on their experiences in these classes;

Surveys of graduates to determine the utility of these classes to their career;

Faculty evaluation of student progress in course work;

Interviews and surveys of internship mentors

Course work for the PSM degree helped students secure industry internships and initial employment;

Students and graduates report applying knowledge from courses to work settings

Graduates enjoy long term success in professional careers

Provide experiential training in academia or industry research or development to prepare students for the expectations of the workplace

Mentored research or development projects in academia, industrial or government settings (Internship)

Surveys of students focusing on their experiences in their internship;

Surveys of graduates to determine the utility of their experiential training to their career;

Faculty advisor and internship mentor evaluation of both

Experiential training prepares students for the workplace and helps them secure their first post-graduation position

Graduates enjoy long term success in academic or professional careers

43

the project and the written reports and presentation;

Interviews and surveys of faculty advisors and internship mentors

Program improvement will be an ongoing process. The results of the assessment measures will be shared with the Bioinformatics Steering Committee, the Bioinformatics Industry Advisory Board and the Bioinformatics Graduate Committee. The curriculum will be modified as necessary to achieve the goal of producing graduates who apply the knowledge, skills and abilities gained from the Professional Science Master’s program in Bioinformatics to their career.

44

PART V

PROGRAM POLICY

STATEMENT

45

I. PROGRAM HISTORY A. RATIONALE The completion of the human genome sequence marked the beginning of a new era of biological research. Scientists have begun to systematically tackle gene functions and other complex regulatory processes by studying organisms at the global scales. Advances in high-throughput biotechnologies and large-scale bioscience have further enabled modeling and simulation over a multitude of length, time and biological scales from biomolecules, cells, tissues and organs to organisms and population. With the enormous volume of data being produced, biology is becoming an increasingly quantitative science. Computational approaches, in combination with experimental methods, have become essential for generating novel hypotheses, deriving new scientific knowledge, and driving discovery and innovation. Bioinformatics & Computational Biology is an emerging field where biological and computational disciplines converge. According to the National Institutes of Health, the working definitions of Bioinformatics and Computational Biology are as follows:

Bioinformatics: Research, development, or application of computational tools and approaches for expanding the use of biological, medical, behavioral or health data, including those to acquire, store, organize, archive, analyze, or visualize such data.

Computational Biology: The development and application of data-analytical and theoretical methods, mathematical modeling and computational simulation techniques to the study of biological, behavioral, and social systems.

Fundamental to the modern day biological studies and key to the basic understanding of complex biological systems, Bioinformatics & Computational Biology is impacting the science and technology of fields ranging from agricultural and environmental sciences to pharmaceutical and medical sciences. The research requires close collaboration among multi-disciplinary teams of researchers in quantitative sciences, life sciences, and their interfaces. According to many accredited scientific and industry reviews, bioinformatics and computational biology may well be the single fastest-growing specialty in the life sciences. The University of Delaware currently does not offer a specialized graduate degree in Bioinformatics & Computational Biology, although related courses have been taught in several departments for a number of years. The Professional Science Master’s program in Bioinformatics & Computational Biology will offer graduate education in a discipline essential for UD as a major research university. According to the International Society for Computational Biology, there are presently 180 bioinformatics-related degree programs worldwide, almost 100 in the United States alone. The Professional Science Master’s program in Bioinformatics will train the next-generation of researchers and professionals who will play a key role in multi- and interdisciplinary teams, bridging life sciences and computational sciences. The program will be administered through its academic home, the Department of Computer & Information Sciences, and will be coordinated by the newly established Center for Bioinformatics & Computational Biology. The scientific curriculum will build upon the research and educational strength from departments across the Colleges of Arts & Sciences, Engineering, Agriculture & Natural Resources, and Earth, Ocean &

46

Environment. The Master’s program will provide a solid foundation for the future development of a PhD degree program in Bioinformatics and Computational Systems Biology. The program will be synergistic to the existing degree programs, providing a critical component to University’s strategic priorities in Energy and Environment studies and Translational Medicine, and serving as a pillar of UD's Path to Prominence.

B. DEGREES OFFERED The Bioinformatics Master’s program will offer the degrees Professional Science Master’s in Bioinformatics (BINF-PSM) with a Computational Sciences Concentration (CS). The Professional Science Master’s in Bioinformatics (BINF-PSM) will position UD as a regional leader in bioinformatics professional education. To address the growing need for highly trained professionals in industry, there is a need for an alternative model of graduate education, which is focused on preparing graduates for nonacademic careers. Over the last decade, the concept of Professional Science Master’s has crystallized as the most effective response to the observed industry dynamic. The “Plus” component of the BINF-PSM will provide training for professional skills for business/industry or for government/non-profit sectors, such as leadership and organization, project management and operations, managerial decision making, intellectual property, and legal and regulatory affairs. These are the “breadth areas” that top the traditional program’s “scientific width”, delivering a so-called T-shaped professional. The scientific curriculum, together with “Plus” component for professional skills and the immersive Internship will prepare the BINF-PSM graduates to pursue a professional career. The Computational Sciences Concentration (CS1) will allow students to gain knowledge and industry experience in developing bioinformatics methods, tools and/or databases for modern biotechnology or medicine. The BINF-PSM graduates will be well positioned to pursue a professional career in industry, business, government agencies, or non-profit organizations.

II. ADMISSION

A. ADMISSION REQUIREMENTS Admission to the graduate program is competitive. Those who meet stated requirements are not guaranteed admission, nor are those who fail to meet all of those requirements necessarily precluded from admission if they offer other appropriate strengths. The following are the admission requirements to the Professional Science Master’s program in Bioinformatics:



47


International student applicants must demonstrate a satisfactory level of proficiency in the English language if English is not the first language. The University requires an official paper-based TOEFL score of at least 550, at least 213 on the computer-based TOEFL, or at least 79 on the Internet-based TOEFL. TOEFL scores more than two years old cannot be considered official;


Applications must also include a resume outlining work and academic experience, as well as an application essay consisting of the answers to the following questions: 1. What educational background and scientific research or employment experience

prepare you for this bioinformatics degree program? 2. What are your long-term professional objectives? 3. What specific attributes of the bioinformatics program make you feel that this degree

is appropriate to help you achieve your professional objectives?

B. APPLICATION Application to the Professional Science Master’s program in Bioinformatics will be submitted using the on-line graduate admission application that includes transcripts from all previous college or university study, letters of recommendation, resume, application essay, and official GRE and TOEFL scores (if applicable). If any part of an application is missing, evaluation of the application cannot begin. The applicant will apply to the Department of Computer & Information Sciences. B.1. APPLICATION DEADLINES Admission decisions are made on a rolling basis as and when applications are complete. Decisions on financial aid awards are usually made in March-May for the Fall Semester, and in November-December for the Spring Semester. The central graduate admissions office continues to process applications and transcripts throughout the year and follows the stated two (2) week processing timeline for all materials received in the office. The application deadlines are:

Fall Semester: July 1st (regular application); March 1st (financial aid) Spring Semester: December 1st (regular application); October 1st (financial aid)

B.2. CHANGE OF CLASSIFICATION Students currently matriculated in other graduate degree programs should complete a “Change of Classification” Form to seek approval to enter the Professional Science Master’s program in Bioinformatics. The Bioinformatics Graduate Committee will evaluate each Change of Classification request on a case-by-case basis and determine whether the student is required to

48

submit a completed admission application form to the Office of Graduate and Professional Education and follow the same procedures for admission as other applicants. C. ADMISSION STATUS Students may be admitted into the Professional Science Master’s program in Bioinformatics with regular status or provisional status. Regular. Regular status is offered to students who meet all of the established entrance requirements, who have a record of high scholarship in their fields of specialization, and who have the ability, interest, and maturity necessary for successful study at the graduate level in a degree program. Provisional. Provisional status is offered to students who are seeking admission to the degree program but lack one or more of the specified prerequisites. All provisional requirements must be met within the deadline given before regular status can be granted. Students admitted with provisional status are generally not eligible for assistantships or fellowships. Students who file an application during the final year of undergraduate or current graduate work and are unable to supply complete official transcripts showing the conferral of the degree will be admitted pending conferral of the degree if their records are otherwise satisfactory and complete. For students lacking appropriate preparatory course work, additional courses applicable to certain areas of study may be required prior to admission or students may be admitted with the provision that completion of certain area content courses be completed concurrent with the courses in the degree program.

III. ACADEMIC

A. DEGREE REQUIREMENTS


15 Credits


12 Credits

B. COURSE CURRICULUM The tables below list the course curriculum for the major components of the Professional Science Master’s program in Bioinformatics. New or revised courses required for the curriculum are

49

marked. All of these courses have been submitted to the Course Challenge list and will be effective for the Fall 2010 term.

BIOINFORMATICS SCIENCE CORE – COMPUTATIONAL SCIENCES Bioinformatics & Computational Biology Core – Computational Sciences (15) Bioinformatics (3) CISC636: Bioinformatics (3) *





CISC636: Bioinformatics (3) * submitted for re-title from “Introduction to Bioinformatics” PLSC636: Plant Genes and Genomes (3) * submitted for re-title from “Advanced Plant Genetics” MATH660: Introduction to Systems Biology (3) * adapted from MATH460 STAT613: Multivariate Statistical Methods with Biology Applications (3) * new course being developed

ETHICS CORE

Ethics Core (3)


BISC631: Practice of Science (3) UAPP648: Environmental Ethics (3) UAPP650: Values Ethics and Leadership (3) BUAD840: Ethical Issues in Global Business Environments (3)

BIOINFORMATICS & COMPUTATIONAL BIOLOGY INTERNSHIP

Internship (6) Internship (6) BINF864: Internship (1-6) *

BINF864: Internship * new course listing

ELECTIVES – COMPUTATIONAL SCIENCES

Electives – Computational Sciences (6)

Electives (6) [select two]

CISC841: Algorithms in Bioinformatics (3) CISC621: Algorithm Design and Analysis (3) CISC640: Computer Graphics (3) CISC642: Introduction to Computer Vision (3) CISC650: Computer Networks (3) CISC675: Object Oriented Software Engineering (3) CISC681: Artificial Intelligence (3)

50

CISC683: Introduction to Data mining (3) CISC882: Natural Language Processing (3) CISC886: Multi-Agent Systems (3) CISC887: Internet Information Gathering (3) CISC888: Machine Learning (3) MATH607: Survey of Scientific Computing (3) MATH611: Introduction to Numerical Analysis and Scientific Computing (3)STAT670: Introduction to Statistical Analysis I (3) * STAT671: Introduction to Statistical Analysis II (3) * STAT608: Statistical Research Methods (3) STAT615: Design and Analysis of Experiments (3) STAT619: Time Series Analysis (3) STAT621: Survival analysis (3) STAT674: Applied Data Base Management (3) ELEG633: Image Processing (3) ELEG652: Principles of Parallel Computer Architectures (3) ELEG655: High-Performance Computing with Commodity Hardware (3) ELEG679: Introduction to Medical Imaging Systems (3) ELEG680: Immunology for Engineers (3) CHEG620: Biochemical Engineering (3) CHEG621: Metabolic Engineering (3)

STAT670: Introduction to Statistical Analysis I (3) * new course being developed STAT671: Introduction to Statistical Analysis II (3) * new course being developed

PROFESSIONAL SCIENCE MASTER’S PLUS COURSES

Professional Science Master’s Plus Courses – Business/Industry Track † (12) Survey of Business (3) BUAD500: Survey of Business (3) * Leadership and Organization (3)









Managerial Decision Making or Financial Management (3) [select one]

UAPP819: Management Decision Making in Public & Nonprofit Sectors (3)UAPP833: Financial Management in Public & Nonprofit Sectors (3) UAPP827: Program and Project Analysis (3) UAPP829: Taxation and Fiscal Policies (3)

Legal and Regulatory UAPP646: Administrative Law and Policy (3)

51

Affairs (3) BUAD500: Survey of Business (3) * new course being developed † Students are recommended to follow one of the tracks, but may cross over tracks to fit interest.

C. COMMITTEES AND DIRECTOR The development, administration and progress assessment of the Professional Science Master’s program in Bioinformatics will be guided by the Director and three committees—the Bioinformatics Steering Committee, the Bioinformatics Industry Advisory Board and the Bioinformatics Graduate Committee, as outlined below. C.1. BIOINFORMATICS STEERING COMMITTEE The Steering Committee will advise the development and progress assessment of the Professional Science Master’s program in Bioinformatics. The committee consists of faculty members from all ten Departments across four Colleges participating in this degree program. Member College Department Expertise

Wu, Cathy (Chair) Arts & Science Computer & Information Sciences

Bioinformatics, Cyberinfrastrcture

Antoniewicz, Maciek Engineering Chemical Engineering Metabolic Engineering, Systems Biology

Bahnson, Brian Arts & Science Chemistry & Biochemistry

Structure Biology, Molecular Modeling

Duncan, Melinda Arts & Science Biological Sciences Biotechnology PSM, Developmental Biology

Hanson, Thomas Earth, Ocean & Environment

Marine Biosciences Microbial Genomics

Lee, Kelvin Engineering Chemical Engineering Systems Biology, Proteomics

Liao, Li Arts & Science Computer & Information Sciences


Marsh, Adam Earth, Ocean & Environment

Marine Biosciences Environmental Bioinformatics

Meyers, Blake Agriculture & Natural Resources

Plant & Soil Sciences Plant Genomics, Bioinformatics

Rejto, Lidia Agriculture & Natural Resources

Food & Resource Economics

Biostatistics

Schleiniger, Gilberto Arts & Science Mathematical SciencesQuantitative Biology BS Major, Mathematical Biology

Schmidt, Carl Agriculture & Natural Resources

Animal & Food Sciences

Avian Genomics

Taufer, Michaela Arts & Science Computer & Information Sciences

Grid Computing, Cloud Computing

Wommack, Eric Agriculture & Natural Resources

Plant & Soil Sciences Viral Genomics

Zurakowski, Ryan Engineering Electrical & Computer Biomedical Engineering

52

Engineering

C.2. BIOINFORMATICS INDUSTRY ADVISORY BOARD The Industry Advisory Board will advise the development and progress assessment of the Professional Science Master’s program in Bioinformatics from industry perspectives. The Board consists of representatives from major regional companies and institutions who will participate in this degree program and have committed to host internships. Member Title Organization Tomb, Jean-Francois (Chair)

Manager – Bioinformatics at DuPont DuPont Central Research & Development

Barbara, Deb VP, New Business Development Strategic Diagnostics, Inc.

Bunnell, Tim Director, Center for Pediatric Auditory & Speech Sciences

duPont Hospital for Children

Christianson, Anastasia

Director of Discovery Medicine Informatics

AstraZeneca

Foutrakis, George Associate, GORE Medical Products W.L. Gore Hollis, Greg VP, Applied Technology Group Incyte

Weintraub, William Director, Christiana Center for Outcomes Research

Christiana Care

Wright, Ian Head of Global Assay Development Siemens Healthcare Diagnostics

C.3. BIOINFORMATICS GRADUATE COMMITTEE The Graduate Committee will be responsible for admission, advising, and progress assessment of the students in the Professional Science Master’s program in Bioinformatics, working closely with the students’ Faculty Advisors. The committee consists of at least two representative faculty members from each participating College in this degree program. Member College Department

Wu, Cathy (Chair) Arts & Sciences Computer & Information Sciences/ Biological Science

Hanson, Thomas Earth, Ocean & Environment Marine Biosciences Lee, Kelvin Engineering Chemical Engineering Liao, Li Arts & Sciences Computer & Information Sciences Papoutsakis, Eleftherios Engineering Chemical Engineering Patel, Sandeep Arts & Sciences Chemistry & Biochemistry Rejto, Lidia Agriculture & Natural Resources Food & Resource Economics Schleiniger, Gilberto Arts & Sciences Mathematical Sciences Schmidt, Carl Agriculture & Natural Resources Animal & Food Sciences

Wommack, Eric Agriculture & Natural Resources/ Earth, Ocean & Environment

Plant and Soil Sciences/ Marine Biosciences

C.4. DIRECTOR

53

The Director of the Professional Science Master’s program in Bioinformatics will be responsible for the overall implementation, quality and progress of the degree program, advised by the Steering Committee and the Industry Advisory Board. The Director will also be the Chair of the Bioinformatics Graduate Committee. We propose that the Director of the Professional Science Master’s program in Bioinformatics be a rotating position. Because of a significant amount of time and effort spent in starting up the program, we propose that the Director be located in Computer & Information Sciences for the first two years to get things started. Then, the position will rotate for a three-year term. The Director may appoint a Coordinator to provide day-to-day program management and assist with student recruitment, admission, advising, progress assessment, and career planning.

D. SATISFACTORY PROGRESS D.1. FACULTY ADVISOR Students are required to choose an appropriate Faculty Advisor from a list of faculty members participating in the degree program or have an appropriate Faculty Advisor appointed by the Director of the Professional Science Master’s program in Bioinformatics. The participating faculty members are faculty approved by the Bioinformatics Steering Committee to advise students and/or serve as research mentors or co-mentors. The list of participating faculty, along with their departments and research interests, are available from the Bioinformatics program web site (http://bioinformatics.udel.edu/Education). The Faculty Advisor will be the primary contact of the student for questions and advice. The student will develop a plan of study for the program with the Faculty Advisor before the beginning of the second semester. The Director of the Professional Science Master’s program in Bioinformatics will verify that the student has completed the requirements for the program and will approve the application for the degree upon successful completion of the requirements. D.2. ACADEMIC LOAD Full-time student is expected to complete BINF-PSM program (42 credits) in two years. The program may be completed over a longer time frame for part-time students. Students enrolled in at least 9 credit hours or in sustaining credit are considered full-time students. Those enrolled for fewer than 9 credit hours are considered part-time students, although students holding assistantships are considered full-time with six credits. Generally, a maximum load is 12 graduate credit hours; however, additional credit hours may be taken with the approval of the student's adviser and the Office of Graduate and Professional Education. A maximum course load in either summer or winter session is 7 credit hours. Permission must be obtained from the Office of Graduate and Professional Education to carry an overload in any session D.3. TRANSFERABILITY

54

Prior to admission to the Professional Science Master’s program in Bioinformatics, a prospective student from another institution can be approved by the Bioinformatics Graduate Committee to take up to 9 graduate credits that, if/when admitted to the degree program, would be applied to that degree. Once the student has successfully completed 9 approved graduate UD credits and been admitted to the degree program, then a maximum of 9 graduate credits, but not the grades or quality points, can be transferred into the Master’s program from another institution with the approval of the Graduate Committee. Students who complete graduate credits with the classification of CEND (Continuing Education Non-degree) at the University of Delaware may use a maximum of 9 graduate credits earned with this classification toward their graduate degree. All requests for transfer credit should be directed to the academic home department, Department of Computer & Information Sciences, using a “Request for Transfer of Graduate Credit” Form. Transfer credits will be accepted provided that such credits: (i) were earned with a grade of no less than B-, (ii) are approved by the Bioinformatics Graduate Committee, (iii) are in accord with the Program Policy Statement of the Professional Science Master’s program in Bioinformatics, (iv) are not older than five years, (v) are graduate level courses, and (vi) were completed at an accredited college or university. Graduate courses counted toward a degree received elsewhere may not be transferred into a degree at UD. Credits from institutions outside of the United States are generally not transferable to UD. D.4. PSM INTERNSHIP The PSM-BINF programs require a 6 month full-time, or a 12 month half-time internship as part of the degree requirements. The capstone internship will be in most cases completed at participating companies/institutions in the Master’s program in Bioinformatics & Computational Biology. Most internship opportunities will be in industries based near UD including locations in Delaware, Southeastern Pennsylvania, Northeastern Maryland and Southern New Jersey. However, since these internships can be full time, students may chose to pursue internships further afield as opportunities arise. The internship will be jointly supervised by a Faculty Advisor at UD and an Internship Mentor in the hosting institution. Unless special permission is granted, students need to complete 12 credit hours prior to the start of their internship. The students, with the assistance of their Faculty Advisor and Internship Mentor, will propose a specific research learning experience for their internship, and have the internship approved by the Director of the Master’s program in Bioinformatics & Computational Biology prior to the start of the internship. The internship research will be assessed by the quality of the work performed at the internship, two written reports—a plan of work and a final research paper, as well as a poster presentation. The plan of work should outline the background of the research project, the learning objectives for the internship and goals to be accomplished. The final 20-page research paper should outline the objectives of internship research, what are accomplished on each objective and recommendations for future work, following the format: Introduction, Research Methods, Results, Discussion/Conclusion, and Reference Citation. The poster presentation will be presented at an annual Research Day at the University of Delaware where MS and PSM students will showcase their thesis and internship projects. The internship will

55

have the same academic rigor of a master thesis, while the emphasis will be on effective problem solving, technological transfer, product development and technical innovation in a team environment at the company setting. The final grade will be assigned by the Faculty Advisor in accordance with UD academic standards. D.5. GRADE REQUIREMENTS Only graduate courses completed with a grade of B or higher count towards the requirements of Bioinformatics Master’s program. Students receiving a B- or lower in a required core course are subject to dismissal from the program. However, they may file an appeal to the Bioinformatics Graduate Committee for approval to retake the course and remain in the program if the appeal is approved. Students must obtain at least a 3.0 cumulative grade point average in the courses in the curriculum to receive the degree. D.6. CONSEQUENCES OF UNSATISFACTORY ACADEMIC PROGRESS The Bioinformatics Graduate Committee will meet at least once each semester to evaluate each student's progress. If a student is failing to make satisfactory progress towards a degree, the committee will recommend suitable action to the Director of the Master’s program in Bioinformatics & Computational Biology. Possible actions include (but are not limited to): (i) requirement for additional courses, (ii) suspension of financial support, and (iii) recommendation for dismissal. D.7. STANDARDS OF STUDENT CONDUCT All graduate students are subject to University of Delaware regulations regarding academic honesty. Violations of the UD regulations regarding academic honesty or other forms of gross misconduct may result in immediate dismissal from the Program. D.8. DISMISSAL The procedures for dismissal as detailed in the University Catalog will be followed. Briefly, the Graduate Committee will report its recommendation and reason for dismissal to the Director of the Professional Science Master’s program in Bioinformatics. The Director will make a recommendation to the Office of Graduate Studies, who will decide whether to dismiss the student. The student may appeal this decision to the Office of Graduate Studies, following the procedure given in the University Catalog. D.9. GRADUATE STUDENT GRIEVANCE PROCEDURES Students who feel that they have been graded inappropriately or receive what they perceive as an unfair evaluation by a faculty member may file grievances in accordance with University of Delaware policies. Students are encouraged to contact the Director of the Professional Science Master’s program in Bioinformatics prior to filing a formal grievance in an effort to resolve the situation informally.

56

D.11. ATTENDANCE AT CONFERENCES AND PROFESSIONAL MEETINGS The Professional Science Master’s program in Bioinformatics encourages students to attend conferences and professional meetings. They provide opportunities to meet future employers and colleagues, and can offer specialized training beyond course work.

IV. FINANCIAL AID

A. FINANCIAL AWARDS Admission to the Professional Science Master’s program in Bioinformatics does not automatically entitle an applicant to financial aid. Students may seek financial aid opportunities, such as fellowships or scholarships from sources within the University and from private and federal agencies. Interested students should check the Office of Graduate Studies for the most current opportunities. Financial aid is awarded on a competitive basis from the pool of admitted applicants. The University of Delaware's policies apply to all forms of financial aid. Please refer to the University Policies for Graduate Student Assistantships and Fellowships. Students in the BINF-PSM program may apply for Industry Internships. Paid internships may be available from industry, government agencies or other participating institutions in the Professional Science Master’s program in Bioinformatics.

57

APPENDIX I

LETTERS OF APPROVAL FROM CONTRIBUTING DEPARTMENTS/UNITS College of Arts & Sciences

1. Dr. David Saunders, Chair, Department of Computer & Information Sciences [Academic Home Department]

2. Dr. Randall Duncan, Chair, Department of Biological Sciences 3. Dr. Peter Monk, Chair, Department of Mathematical Sciences 4. Dr. Klaus Theopold, Chair, Department of Chemistry & Biochemistry

College of Agriculture & Natural Resources

5. Dr. Jack Gelb Jr., Chair, Department of Animal & Food Sciences 6. Dr. Thomas Ilvento, Chair, Department of Food & Resource Economics 7. Dr. Blake Meyers, Interim Chair, Department of Plant & Soil Sciences

College of Engineering

8. Dr. Kenneth Barner, Chair, Department of Electrical & Computer Engineering 9. Dr. Norman Wagner, Chair, Department of Chemical Engineering

College of Earth, Ocean & Environment

10. Dr. Charles Epifanio, Director, School of Marine Science and Policy College of Health Sciences

11. Dr. Susan Hall, Chair, Department of Health, Nutrition & Exercise Sciences 12. Dr. Stuart Binder-Macleod, Chair, Department of Physical Therapy

Alfred Lerner College of Business & Economics

13. Dr. Rick Andrews, Chair, Department of Business Administration 14. Dr. Guido Geerts, Chair, Department of Accounting & management Information Systems

College of Education & Public Policy

15. Dr. Maria Aristigueta, Director, School of Urban Affairs & Public Policy Office of the Vice Provost for Graduate & Professional Education

16. Dr. John Sawyer, Associate Provost for Professional Education

58

APPENDIX II

LETTERS OF SUPPORT FROM DEANS OF PARTICIPATING COLLEGES

1. Dr. George H. Watson, Interim Dean, College of Arts & Sciences 2. Dr. Robin W. Morgan, Dean, College of Agriculture & Natural Resources

3. Dr. Michael J. Chajes, Dean, College of Engineering

4. Dr. Nancy M. Targett, Dean, College of Earth, Ocean & Environment

UNIVERSITY OF

DELAWARE Department of Computer and Information SciencesUniversity of Delaware103 Smith HallNewark, DE 19716(302) [email protected]

October 15, 2009

Cathy H. Wu, Ph.D.Edward G. Jefferson Professor of Bioinformatics & Computational BiologyDepartment of Computer & Information SciencesDelaware Biotechnology InstituteUniversity of Delaware15 Innovation Way, Suite 205Newark, DE 19711

Dear Cathy,

The Department of Computer and Information Sciences is pleased to support core and elective coursesfor the proposed Professional Science Masters in Bioinformatics (BINF-PSM) and Masters of Science inBioinformatics and Computational Biology (BICB-MS) degree programs and for the Graduate Certificate inBioinformatics (BINF-CERT).

In particular, as we have discussed, we will work together to ensure that the courses CISC636 Bioinformaticsand CISC637 Database Systems will be taught in such a way (1) to be accessible to students of varied degreesof preparation in computation and biology and (2) to continue to provide rigorous training in these subjectsfor CIS graduate students and BINF/BICB students alike.

The elective CISC6xx courses listed are normally taught every year, some of them every semester. Likewisethe CISC8xx course electives usually are offered each year, though occasionally they appear 3 or 4 semestersapart. Courses do sometimes fill to capacity, but I anticipate that our schedule of offerings and the numberof seats available will provide a rich set of options for students in this program without difficulty.

The Department of Computer and Information Sciences is pleased to contribute to the education of studentsin this important area. These programs will be a benefit to the University of Delaware and to our society.

Sincerely,

B. David Saunders

Randall L. Duncan, Ph.D. Professor and Chairman Department of Biological Sciences 118C Wolf Hall Telephone (302) 831-6977 Fax No. (302) 831-1033 E-mail: [email protected]

October 12, 2009 Cathy H. Wu, Ph.D. Edward. G. Jefferson Chair Professor, Computer & Information Sciences and Professor, Biological Sciences Delaware Biotechnology Institute 15 Innovation Way, Suite 205 University of Delaware Newark, DE 19711 Dear Cathy, We shall be happy to make available seats in graduate courses in Biological Sciences, which will serve as electives in your proposed Masters of Science degree in Bioinformatics. As a proviso, I cannot guarantee the availability of space for all comers at all times since some of the listed courses often reach their enrollment limits. However, several courses on the list seldom reach enrollment limits and we are willing to consider increasing the available sections for the most popular graduate classes in the future if there is sufficient demand. Please let me know if you require anything else in this regard. We wish you much success with this new initiative. Best regards,

Professor and Chair

Randall L. Duncan, Ph.D. Professor and Chairman Department of Biological Sciences 118C Wolf Hall Telephone (302) 831-6977 Fax No. (302) 831-1033 E-mail: [email protected]

October 13, 2009 Cathy H. Wu, Ph.D. Edward. G. Jefferson Chair Professor, Computer & Information Sciences and Professor, Biological Sciences Delaware Biotechnology Institute 15 Innovation Way, Suite 205 University of Delaware Newark, DE 19711 Dear Cathy, We shall be happy to make available seats in graduate courses in Biological Sciences, which will serve as electives in your proposed Professional Science Masters degree in Bioinformatics. As a proviso, I cannot guarantee the availability of space for all comers at all times since some of the listed courses often reach their enrollment limits. However, several courses on the list seldom reach enrollment limits and we are willing to consider increasing the available sections for the most popular graduate classes in the future if there is sufficient demand. Please let me know if you require anything else in this regard. We wish you much success with this new initiative. Best regards,

Professor and Chair

e-mail: [email protected]

September 30, 2009 Cathy H. Wu, Ph.D. Edward G. Jefferson Professor of Bioinformatics & Computational Biology Department of Computer & Information Sciences Delaware Biotechnology Institute University of Delaware 15 Innovation Way, Suite 205 Newark, DE 19711 Dear Prof. Wu: The Department of Chemistry & Biochemistry strongly supports enrollment of students in our graduate level courses that are listed as electives for your proposed Professional Science Masters in Bioinformatics (BINF-PSM) and Masters of Science in Bioinformatics and Computational Biology (BICB-MS) degree programs. The Department has submitted a proposal for the regularization of CHEM 684 titled Biochemistry of Nucleic Acids, which will be offered each spring semester. You may consider adding this course to your list of electives. Each of the courses that are listed in your BINF-PSM or BICB-MS program under the Life Sciences elective are offered once per year. The courses CHEM 641 (Biochemistry), CHEM 645 (Protein Structure and Function) and CHEM 646 (DNA-Protein Interactions) are offered in the fall semester. The CHEM 641 course has two sections open. The courses CHEM 624 (Principles of Mass Spectrometry) and CHEM 649 (Molecular Biophysics) are offered each spring. These courses typically have room for additional enrollment, and we would welcome BINF-PSM and BICB-MS enrollment to fill open seats in these classes. The Department of Chemistry & Biochemistry is excited to be a part of this initiative and looks forward to teaching students from these new programs. With best regards,

Klaus H. Theopold Professor and Chair

COLLEGE OF AGRICULTURE AND NATURAL RESOURCES

Thomas W. Ilvento 213 Townsend Hall University of Delaware Newark, DE 19716-2130 Ph: 302-831-6773 Fax: 302-831-6243 [email protected]

A N E Q U A L O P P O R T U N I T Y U N I V E R S I T Y

STATISTICS PROGRAM ProgramoogramProgram Program

October 13, 2008

Cathy H. Wu, Ph.D. Edward G. Jefferson Professor of Bioinformatics & Computational Biology Center for Bioinformatics and Computational Biology (CBCB) Dear Dr. Wu, The Department of Food and Resource Economics will support the following courses for inclusion in the Masters in Bioinformatics and the Profession Science Masters in Bioinformatics. By supporting these courses we acknowledge our intent to teach these courses on a regular basis and to admit nonmajors into these course as appropriate. STAT 608 Statistical Research Methods I STAT 615 Design and Analysis of Experiments STAT 619 Time Series Analysis STAT 621 Survival Analysis STAT 656 Biostatistics STAT 674 Applied Data Management The following courses are under the process for revision or a new course. We expected these to be approved in this fiscal year STAT 670 Introduction to Statistical Analysis I STAT 671 Introduction to Statistical Analysis II STAT 613 Multivariate Statistical Methods with Biological Applications Please call or e-mail if you have any further questions or need anything else from me. Sincerely,

Thomas W. Ilvento Professor and Chair, Department of Food and Resource Economics

DEPARTMENT OF PLANT AND SOIL SCIENCES University of Delaware

Newark, DE 19717-1303 OFFICE OF THE CHAIR Ph:302/831-8153

Fax: 302/831-0605 Email: [email protected]

September 28, 2009 The Department of Plant & Soil Sciences is pleased to support breadth courses for Professional Science Master’s (PSM) degree programs. PLSC636: Advanced Plant Genetics is offered during the fall semester. This course is an advanced survey of genetics and genomics in higher plants, including molecular methods of plant biotechnology. Topics include genome composition and evolution, disease resistance, transposable elements and retrotransposons, DNA methylation and epigenetics, quantitative traits, chromosome structure and gene expression. One section of the course is offered each year, and PSM may utilize open seats in existing classes. PLSC644: Physiology of Plant Stress will be offered during either the fall or spring semester. This course focuses on the response of plants to biotic and abiotic environmental stresses; mineral nutrients, salt, drought, cold, heat, light, pathogens and herbivores at the physiological and molecular levels. At least one section of the course is offered each year, and PSM may utilize open seats in existing classes. PLSC667: Analytical Plant Genetics will be offered during either the fall or spring semester and is listed as a seminar course only because it is new. It will be taught as a regular course in the coming years. The Department Plant and Soil Sciences is excited to be a part of this initiative and looks forward to seeing PSM and other students in the classroom. Sincerely,

Blake Meyers Professor

AN EQUAL OPPORTUNITY UNIVERSITY

October 12, 2009 Prof. Cathy Wu Jefferson Chair in Bioinformatics Director, Center for Bioinformatics and Computational Biology Department of Computer and Information Sciences Dear Professor Wu: The School of Marine Science and Policy is pleased to support core courses for the Professional Science Master’s (PSM) and Master of Science degree programs and Graduate Certificate program in Bioinformatics and Computational Biology. Prof. Adam Marsh, within the Marine Biosciences Program, has submitted two course proposals that will provide part of the core curriculum for the Life Sciences concentrations within each of these programs. These are MAST697: Bioinformatics Programming for Biologists and MAST698: Environmental and Systems Bioinformatics. MAST697 will serve as an entry point for biologists who have used bioinformatics tools that are seeking to acquire skills to customize these tools, collect them into pipelines and develop their own tools by developing basic proficiency in PERL, R, and Python languages that are commonly applied in bioinformatics. MAST698 will serve as an overview of bioinformatic analyses for “-omics” data: genomics, transcriptomics, and proteomics. The course will focus on the analysis of real world data sets so that students are exposed to realistic challenges in analyzing the staggering amounts of data produced by these techniques. Prof. Thomas Hanson will co-teach MAST698 with Prof. Marsh. The School of Marine Science and Policy strongly supports this initiative. We expect that the courses above will be subscribed by not only Bioinformatics and Computational Biology students, but will also attract students from SMSP, particularly the Marine Biosciences Program, and other life science programs where students need to apply these techniques to their own research questions. Sincerely,

Charles E. Epifanio, Director School of Marine Science and Policy

October 16, 2009 Cathy H. Wu, Ph.D. Edward G. Jefferson Professor of Bioinformatics & Computational Biology Department of Computer & Information Sciences Delaware Biotechnology Institute University of Delaware 15 Innovation Way, Suite 205 Newark, DE 19711 Dear Professor Wu, The Department of Health, Nutrition, and Exercise Sciences is pleased to support your proposal for the Masters Program in Bioinformatics and Computational Biology. Specifically, we will allow students in the program enrollments in elective courses HESC602, Data Analysis and Interpretation in Health Sciences, and HESC654, Medical Physiology. We wish you success with the program. Sincerely,

Susan J. Hall Professor and Department Chair

PHYSICAL THERAPY

301 McKinly Laboratory University of Delaware Newark, Delaware 19716-2591 Ph: 302/831-8046 Fax: 302/831-4234

October 13, 2009 Cathy H. Wu, Ph.D. Edward G. Jefferson Professor of Bioinformatics & Computational Biology Department of Computer & Information Sciences Delaware Biotechnology Institute University of Delaware 15 Innovation Way, Suite 205 Newark, DE 19711 Dear Prof. Wu: Welcome to the University of Delaware. The Department of Physical Therapy is very pleased to support your efforts in the development a new Master’s program for in Bioinformatics and would welcome students from the program to take appropriate elective courses within the Department. As we discussed, we believe appropriate courses would include: PHYT633 -Applied Physiology II, PHYT623 – Clinical Neuroscience, and PHYT606 – Research. The Department of Physical Therapy is excited to be a part of this initiative and looks forward to teaching students from this new program. Sincerely,

Stuart Binder-Macleod, PT, PhD, FAPTA Edward L. Ratledge Professor and Chair Department of Physical Therapy

Dr. Rick L. Andrews Phone: (302) 831-1190 Deputy Dean, Lerner College of Business & Economics Fax: (302) 831-4196 Chair, Department of Business Administration Email: [email protected] Professor of Marketing website: http://www.buec.udel.edu/andrews/ Lerner College of Business & Economics University of Delaware Newark, DE 19716

September 8, 2009

The Department of Business Administration is pleased to support breadth courses for Professional Science Master’s (PSM) degree programs. The Department has submitted a proposal for a new breadth course, BUAD500 (SURVEY OF BUSINESS). Starting Spring 2011, one section of the course will be offered every year. The course will be available to PSM and other graduate students across campus who are not matriculated in graduate programs in the Lerner College of Business & Economics. BUAD840 (ETHICAL ISSUES IN DOMESTIC AND GLOBAL BUSINESS ENVIRONMENTS) is offered during Fall and Spring semesters. Three or four sections of the course are offered each year, and PSM may utilize open seats in existing classes. BUAD870 (LEADERSHIP AND ORGANIZATIONAL BEHAVIOR) is offered during Fall and Spring semesters. At least four sections of the course are offered each year, and PSM may utilize open seats in existing classes. BUAD835 (MANAGING NEW PRODUCT DEVELOPMENT PROJECTS), BUAD831 (OPERATIONS MANAGEMENT AND MANAGEMENT SCIENCE) and BUAD871 (MANAGING FOR CREATIVITY AND INNOVATION) are options among a set of five courses; demand for these courses can be spread to use seats in available sections. BUAD831 and BUAD871 are offered regularly, while BUAD835 will be offered less frequently (not more than once per year and perhaps not every year). The Department of Business Administration is excited to be a part of this initiative and looks forward to seeing PSM and other students in the classroom. Regards,

Dr. Rick L. Andrews

Lerner College of Business & Economics

Department of Business Administration

September 30, 2009

John E. Sawyer, Ph.D. Associate Provost for Professional Education Office of Graduate and Professional Education & Professor & Director - Organizational Effectiveness, Development, and Change Department of Business Administration Alfred Lerner College of Business & Economics 320 Lerner Hall University of Delaware Newark, DE 19716

Dear Professor Sawyer:

The faculty of the School of Urban Affairs and Public Policy voted unanimously to enthusiastically support the Professional Science Master’s Program (PSM Plus). I have reviewed the proposal and this program requires a selection from the following courses in the Government/Non-Profit track—UAPP 803, UAPP835, UAPP604, UAPP819, UAPP833, UAPP827, UAPP829, UAPP646, UAPP648 and UAPP650. We will make these courses available to the PSM Plus students on semesters in which they offered.

I look forward to working with you on this major and on other collaborations in the future.

Regards,

Maria P. Aristigueta Professor and Director School of Urban Affairs and Public Policy

October 15, 2009 Cathy H. Wu, Ph.D. Edward. G. Jefferson Chair Professor, Computer & Information Sciences and Professor, Biological Sciences Delaware Biotechnology Institute 15 Innovation Way, Suite 205 University of Delaware Newark, DE 19711 Dear Cathy, We are pleased about the bioinformatics graduate programs you are proposing. The MS, Professional Science Master’s (PSM) and Certificate provide an excellent array of options to meet a variety of student situations and motivations. These programs will also meet a critical need of idustry for trained professionals in our region. I am especially excited about the Professional Science Master’s (PSM) option. As you know, growing and enhancing graduate professional education is one of the milestones of the Path to Prominence. I believe that the PSM in Bioinformatics will be a key component of the University’s portfolio of graduate professional education options, and fits very well with our industry, health care and government partnerships. Sincerely,

John E. Sawyer, Ph.D. Associate Provost for Professional Education

Office of Graduate & Professional Education

Associate Provost Professional Education

University of Delaware Newark, Delaware 19716-2710 Ph: 302-831-4377 Fax: 302-831-8745 E-mail: [email protected]

College of Engineering 102 DuPont Hall

University of Delaware Newark, Delaware 19716

November 19, 2009 Prof. Cathy Wu Department of Computer & Information Sciences University of Delaware Newark, DE 19716 RE: Proposed Master’s Program in Bioinformatics & Computational Biology

Dear Cathy,

I am very pleased to be able to provide the support of the College of Engineering for the proposed Master’s degree programs—Master of Science in Bioinformatics & Computational Biology (BICB-MS), Professional Science Master’s in Bioinformatics (BINF-PSM), and Graduate Certificate in Bioinformatics (BINF-CERT). You have put together an excellent proposal, and there is no doubt that these programs are of extremely high quality. I thank you for your efforts as these programs will be a great addition to our graduate degree offerings here at UD.

We look forward to supporting your efforts as the programs move forward.

Cordially,

Michael J. Chajes, Dean and Professor

21 November 2009 Professor Cathy Wu Delaware Biotechnology Institute University of Delaware Newark, DE 19716 Dear Cathy, I am pleased to strongly endorse the M.S. program that you propose in Bioinformatics and Computational Biology. You have put together a compelling rationale and a very thorough case in support of this new degree program. CEOE, through its relevant programs, is very pleased to be a participant. Sincerely,

Nancy M. Targett, Ph.D. Dean

professional science master’s in bioinformatics ... · quantitative sciences background to gain...

Documents